sequence alignment

Summary

Summary: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.

Top Publications

  1. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
  2. ncbi Clustal W and Clustal X version 2.0
    M A Larkin
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 23:2947-8. 2007
  3. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
  4. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
  5. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
  6. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
  7. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
  8. ncbi UCSF Chimera--a visualization system for exploratory research and analysis
    Eric F Pettersen
    Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
    J Comput Chem 25:1605-12. 2004
  9. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
  10. pmc MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    Kazutaka Katoh
    Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
    Mol Biol Evol 30:772-80. 2013

Detail Information

Publications291 found, 100 shown here

  1. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
    The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms...
  2. ncbi Clustal W and Clustal X version 2.0
    M A Larkin
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 23:2947-8. 2007
    SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++...
  3. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
    ..The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle...
  4. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  5. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
    ..Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu)...
  6. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
    ..The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively...
  7. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
    ..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
  8. ncbi UCSF Chimera--a visualization system for exploratory research and analysis
    Eric F Pettersen
    Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
    J Comput Chem 25:1605-12. 2004
    ..Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/...
  9. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
    ..for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing ..
  10. pmc MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    Kazutaka Katoh
    Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
    Mol Biol Evol 30:772-80. 2013
    We report a major update of the MAFFT multiple sequence alignment program...
  11. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  12. ncbi The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Konstantin Arnold
    Biozentrum Basel, University of Basel Switzerland
    Bioinformatics 22:195-201. 2006
    ....
  13. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009
    ..Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from ..
  14. pmc MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    Kazutaka Katoh
    Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
    Nucleic Acids Res 30:3059-66. 2002
    A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques...
  15. ncbi Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    J Castresana
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 17:540-52. 2000
    ....
  16. pmc FastTree 2--approximately maximum-likelihood trees for large alignments
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
    PLoS ONE 5:e9490. 2010
    ..We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability...
  17. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
    ..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
  18. ncbi SOAP2: an improved ultrafast tool for short read alignment
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China
    Bioinformatics 25:1966-7. 2009
    ..Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome...
  19. pmc MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    Robert C Edgar
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    BMC Bioinformatics 5:113. 2004
    ..We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles...
  20. pmc MAFFT version 5: improvement in accuracy of multiple sequence alignment
    Kazutaka Katoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 33:511-8. 2005
    The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5...
  21. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
    ..This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer...
  22. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria...
  23. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
    ..The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals...
  24. doi jModelTest: phylogenetic model averaging
    David Posada
    Mol Biol Evol 25:1253-6. 2008
    ..The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es...
  25. pmc SIFT: Predicting amino acid changes that affect protein function
    Pauline C Ng
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A1 162, Seattle, WA 98109, USA
    Nucleic Acids Res 31:3812-4. 2003
    ..We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html...
  26. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
    ..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
  27. ncbi Recent developments in the MAFFT multiple sequence alignment program
    Kazutaka Katoh
    Digital Medicine Initiative, Kyushu University, Fukuoka 812 8582, Japan
    Brief Bioinform 9:286-98. 2008
    The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics...
  28. pmc I-TASSER server for protein 3D structure prediction
    Yang Zhang
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
    BMC Bioinformatics 9:40. 2008
    ..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions...
  29. pmc Phylogeny.fr: robust phylogenetic analysis for the non-specialist
    A Dereeper
    Information Génomique et Structurale IGS, CNRS UPR2589, IFR 88, Marseille, France
    Nucleic Acids Res 36:W465-9. 2008
    ..A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/..
  30. pmc BLAST+: architecture and applications
    Christiam Camacho
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    BMC Bioinformatics 10:421. 2009
    ..There are also some shortcomings in the user-interface of the current command-line applications...
  31. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific ..
  32. ncbi SOAP: short oligonucleotide alignment program
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
    Bioinformatics 24:713-4. 2008
    ..SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets...
  33. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  34. ncbi An improved general amino acid replacement matrix
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universite Montpellier II, Montpellier, France
    Mol Biol Evol 25:1307-20. 2008
    ..Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG...
  35. pmc An efficient algorithm for large-scale detection of protein families
    A J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 30:1575-84. 2002
    ..The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins...
  36. ncbi ACT: the Artemis Comparison Tool
    Tim J Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 21:3422-3. 2005
    ..ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows...
  37. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  38. pmc Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    Fabian Sievers
    School of Medicine and Medical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
    Mol Syst Biol 7:539. 2011
    ..Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam...
  39. pmc Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
    ....
  40. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
    ..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
  41. pmc SWISS-MODEL: An automated protein homology-modeling server
    Torsten Schwede
    Biozentrum der Universitat Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 31:3381-5. 2003
    ..The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server...
  42. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/)...
  43. ncbi HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
    ..AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  44. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ..to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.
  45. ncbi A new generation of homology search tools based on probabilistic inference
    Sean R Eddy
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Genome Inform 23:205-11. 2009
    ..HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm...
  46. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution.
  47. pmc FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, USA
    Mol Biol Evol 26:1641-50. 2009
    ..In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree...
  48. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    ..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
  49. pmc Predicting deleterious amino acid substitutions
    P C Ng
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 11:863-74. 2001
    ..may be used to identify plausible disease candidates among the SNPs that cause missense substitutions...
  50. ncbi T-Coffee: A novel method for fast and accurate multiple sequence alignment
    C Notredame
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Mol Biol 302:205-17. 2000
    We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives...
  51. pmc The Jpred 3 secondary structure prediction server
    Christian Cole
    School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
    Nucleic Acids Res 36:W197-201. 2008
    ..5%. Given either a single protein sequence or a multiple sequence alignment, Jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility ..
  52. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
  53. ncbi ESPript: analysis of multiple sequence alignments in PostScript
    P Gouet
    Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
    Bioinformatics 15:305-8. 1999
    ..It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information...
  54. pmc Rfam: Wikipedia, clans and the "decimal" release
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
    Nucleic Acids Res 39:D141-5. 2011
    ..We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk...
  55. pmc CDD: specific functional annotation with the Conserved Domain Database
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D205-10. 2009
    ....
  56. pmc PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    Mikita Suyama
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 34:W609-12. 2006
    ..The server takes a protein sequence alignment and the corresponding DNA sequences as input...
  57. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  58. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  59. pmc SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes
    Elmar Pruesse
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstr 1, 28359 Bremen, Germany
    Bioinformatics 28:1823-9. 2012
    ..Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements...
  60. ncbi Automatic annotation of organellar genomes with DOGMA
    Stacia K Wyman
    Department of Computer Sciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 20:3252-5. 2004
    ..Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank...
  61. pmc TM-align: a protein structure alignment algorithm based on the TM-score
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
    Nucleic Acids Res 33:2302-9. 2005
    ..This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align...
  62. pmc Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 16:2001-19. 2004
    ....
  63. ncbi Discovering microRNAs from deep sequencing data using miRDeep
    Marc R Friedländer
    Max Delbruck Centrum fur Molekulare Medizin, Robert Rossle Strasse 10, D 13125 Berlin Buch, Germany
    Nat Biotechnol 26:407-15. 2008
    ..miRDeep reports altogether approximately 230 previously unannotated miRNAs, of which four novel C. elegans miRNAs are validated by northern blot analysis...
  64. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    ..Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
  65. pmc CD-HIT Suite: a web server for clustering and comparing biological sequences
    Ying Huang
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 26:680-2. 2010
    ..Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels...
  66. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  67. pmc Tablet--next generation sequence assembly visualization
    Iain Milne
    Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
    Bioinformatics 26:401-2. 2010
    ..Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine...
  68. pmc Genome-wide analysis of the ERF gene family in Arabidopsis and rice
    Toshitsugu Nakano
    Molecular and Cellular Breeding Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305 8566, Japan
    Plant Physiol 140:411-32. 2006
    ..These results will be useful for future functional analyses of the ERF family genes...
  69. pmc Rfam: updates to the RNA families database
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nucleic Acids Res 37:D136-40. 2009
    ..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
  70. ncbi Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  71. pmc SSAHA: a fast search method for large DNA databases
    Z Ning
    Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 11:1725-9. 2001
    ..The SSAHA algorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly. Also, it provides Web-based sequence search facilities for Ensembl projects...
  72. ncbi Next-generation DNA sequencing
    Jay Shendure
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Nat Biotechnol 26:1135-45. 2008
    ....
  73. ncbi Profile hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Bioinformatics 14:755-63. 1998
    ..Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences...
  74. ncbi Automated phylogenetic detection of recombination using a genetic algorithm
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, USA
    Mol Biol Evol 23:1891-901. 2006
    ..We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies ..
  75. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
    Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement...
  76. ncbi Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
    Thomas Huber
    ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
    Bioinformatics 20:2317-9. 2004
    ..Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments...
  77. ncbi Multiple alignment of DNA sequences with MAFFT
    Kazutaka Katoh
    Digital Medicine Initiative, Kyushu University, Fukuoka, Japan
    Methods Mol Biol 537:39-64. 2009
    ..large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program...
  78. pmc BFAST: an alignment tool for large scale genome resequencing
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
    PLoS ONE 4:e7767. 2009
    ..Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation...
  79. pmc trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    Salvador Capella-Gutierrez
    Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain
    Bioinformatics 25:1972-3. 2009
    ..Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized...
  80. pmc Parallelization of the MAFFT multiple sequence alignment program
    Kazutaka Katoh
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    Bioinformatics 26:1899-900. 2010
    Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses...
  81. pmc NCBI BLAST: a better web interface
    Mark Johnson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:W5-9. 2008
    ..Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement...
  82. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..PANTHER/LIB is a collection of "books," each representing a protein family as a multiple sequence alignment, a Hidden Markov Model (HMM), and a family tree...
  83. ncbi Consed: a graphical tool for sequence finishing
    D Gordon
    Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195 7730, USA
    Genome Res 8:195-202. 1998
    ..More information is available at http:// www.genome.washington.edu/consed/consed. html...
  84. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  85. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
    ..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
  86. pmc Fast and accurate long-read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 26:589-95. 2010
    ..For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time...
  87. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
    ..elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction...
  88. ncbi GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
    ..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
  89. pmc GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    Patricia P Chan
    Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE 2, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 37:D93-7. 2009
    ..The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu...
  90. pmc A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    Sean R Eddy
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 4:e1000069. 2008
    ..Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (lambda) ..
  91. ncbi Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
    Jerome C Regier
    Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
    Nature 463:1079-83. 2010
    ..These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships...
  92. pmc Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
    Wei Wang
    Department of Biology and the State Key Lab for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, PR China
    BMC Genomics 10:465. 2009
    ..The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available in this non-model plant species...
  93. ncbi RDP2: recombination detection and analysis from sequence alignments
    D P Martin
    Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town 7000, South Africa
    Bioinformatics 21:260-2. 2005
    ....
  94. ncbi Identification of a differential gene HUMMLC2B between F1 hybrids Landrace x Yorkshire and their female parents Yorkshire
    D Q Xu
    Agriculture Ministry Key Laboratory of Swine Genetics and Breeding, College of Animal Science, Huazhong Agricultural University, Wuhan 430070, China
    Gene 352:118-26. 2005
    ..RT-PCR analysis showed a tissue-specific pattern of expression in skeletal muscle and a similar level of expression during skeletal muscle development. The possible role of HUMMLC2B and its relation to porcine heterosis are discussed...
  95. ncbi A transmembrane phospholipase D in Phytophthora; a novel PLD subfamily
    Harold J G Meijer
    Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, Binnenhaven 5, NL 6709 PD Wageningen, The Netherlands
    Gene 350:173-82. 2005
    ..Since Phytophthora PLD1 cannot be categorized in one of the two existing subfamilies we propose to create a novel subfamily named PXTM-PLD...
  96. ncbi Two distinct teleost hepatocyte nuclear factor 1 genes, hnf1alpha/tcf1 and hnf1beta/tcf2, abundantly expressed in liver, pancreas, gut and kidney of zebrafish
    Hong Yi Gong
    Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
    Gene 338:35-46. 2004
    ..Our results indicate that distinct hnf1alpha and hnf1beta genes in teleosts had been evolved from the hnf1 ancestor gene of chordate...
  97. ncbi Characterization of the mouse Abcc12 gene and its transcript encoding an ATP-binding cassette transporter, an orthologue of human ABCC12
    Hidetada Shimizu
    Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta 4259, Midori ku, 226 8501, Yokohama, Japan
    Gene 310:17-28. 2003
    ..In spite of the genes coding for both ABCC11 and ABCC12 being tandemly located on human chromosome 16q12.1, no putative mouse orthologous gene corresponding to the human ABCC11 was detected at the mouse chromosome 8D3 locus...
  98. ncbi Identification of allelic variants of the bovine immune regulatory molecule CEACAM1 implies a pathogen-driven evolution
    Robert Kammerer
    Tumor Immunology Laboratory, Department of Urology, Klinikum Grosshadern, Ludwig Maximilians University, Marchioninistr 23, Munich D 81377, Germany
    Gene 339:99-109. 2004
    ..This is consistent with the notion that CEACAM1 serves or has served as a pathogen receptor in cattle...
  99. ncbi Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of Anticarsia gemmatalis nucleopolyhedrovirus
    Caren Cristina Dalmolin
    EMBRAPA Recursos Geneticos e Biotecnologia, Parque Estação Biológica PqEB, W5 Norte Final, CEP 70770 900 Brasilia DF, Brazil
    Virus Res 110:99-109. 2005
    ....
  100. ncbi Emergence of Talanin protein associated with human uric acid nephrolithiasis in the Hominidae lineage
    Fernando Gianfrancesco
    Institute of Population Genetics, CNR, Alghero, Italy
    Gene 339:131-8. 2004
    ....
  101. ncbi [Characterization of the beta-actin gene of the rice field eel and its phylogeny in fish]
    Lai Xin Xia
    Center for Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
    Yi Chuan Xue Bao 32:689-95. 2005
    ..The results that suggest lineage-specific beta-actin loss might happen in the radical evolution of teleost fishes...

Research Grants63

  1. Bioconductor: an open computing resource for genomics
    Martin Morgan; Fiscal Year: 2010
    ..which typically are used in microarray analysis, to annotation tools, to plotting functions, GUIs, to sequence alignment and data management packages...
  2. A Fluorescence Polarization Assay for Fatty Acid Adenylating Enzymes
    Courtney C Aldrich; Fiscal Year: 2012
    ..Based on sequence alignment and functional characterization, the mycobacterial FadD's have been divided into 2 classes of ..
  3. Characterization of CHD family chromodomains Implicated in Epigenetic Signaling
    Kimberly R Wiggins; Fiscal Year: 2010
    ..A structure based sequence alignment in the chromodomains of CHD proteins has suggested that the family can be divided into three groups...
  4. High Performance Validation and Classification of Metagenomic Ribosomal-RNA Seque
    Daniel Frank; Fiscal Year: 2011
    ..Rigorous rRNA sequence alignment is a strict requirement for accurate sequence-based phylogenetic classification of microorganisms in ..
  5. Beta2 Integrin Activation and Signaling
    Vineet Gupta; Fiscal Year: 2010
    ..b>Sequence alignment between various integrins shows that there are a number of conserved residues between the betaTD and the ..
  6. Position Sensitive P-Mer Frequency Clustering with Applications to Classification
    Monnie McGee; Fiscal Year: 2012
    ..Current techniques have several shortcomings which need to be addressed. Techniques involving sequence alignment are typically based on selection of one representative sequence (as is typically done when looking at 16S ..
  7. Determining the role of WDR36 in adult-onset primary open-angle glaucoma
    Jonathan M Skarie; Fiscal Year: 2010
    ..The function of the gene and its role in disease pathogenesis are unknown, but sequence alignment and domain structure analysis have lead to the hypothesis that it is the homolog of the yeast nucleolar gene,..
  8. Predictive Structure-Based Models of Malaria Resistance
    David Hecht; Fiscal Year: 2013
    ..for each of these ancestral sequences that will be added sequentially to an already existing structure-based sequence alignment generated from a superposition of experimentally determined x-ray crystal structures of wild-type (wt) DHFR ..
  9. Comparative Bioinformatics and TP53 Expression
    PETER WADDELL; Fiscal Year: 2009
    ..Use, test, and develop bioinformatic/genomic and molecular evolutionary techniques on the dense sequence alignment of (1), plus genomes of over 14 species of mammals...
  10. CSHL Computational and Comparative Genomics Course
    David J Stewart; Fiscal Year: 2012
    ..approaches to genome annotation and analysis, including protein sequence database searching, multiple sequence alignment, identification of promoters and other genetic regulatory elements, and the integration of sequence ..
  11. Bridging Sequence Patterns and Structural Dynamics
    Ivet Bahar; Fiscal Year: 2011
    ..Over the previous funding period, in contrast to conventional methods that employ sequence alignment methods, we undertook an alignment-independent classification approach building on information theory and a ..
  12. A New Approach to Phylogenetic Analysis Using Structural Information
    Abel Rodriguez; Fiscal Year: 2013
    ..community has started to realize that standard procedures for phylogenetic analysis, which first construct a sequence alignment and then use this single point estimate to guide the construction of the phylogenetic tree, can introduce ..
  13. Detecting Homology in the "Twilight Zone" of Sequence Similarity
    RANDEN LEE PATTERSON; Fiscal Year: 2012
    ..used to derive distance estimates and hence phylogenetic relationships without prior information, multiple sequence alignment, or manual editing...
  14. IMPROVE GENOME ANNOTATION USING MULTIPLE SEQUENCE ALIGNMENT RELIABILITY SCORES
    Jian Ma; Fiscal Year: 2013
    ..The foundation of cross-species comparative genomics is multiple sequence alignment (MSA). Despite of the progress in the past decade, MSA is still a difficult task and error-prone...
  15. Structural Alignment of RNA Sequences with Applications
    Gaurav Sharma; Fiscal Year: 2013
    ..iterative computational framework that computes probabilistic representations of RNA folding and inter-sequence alignment and iterates - updating alignments using folding information and vice versa...
  16. Techniques to Integrate Disparate Data: Clinical Personalized Pragmatic Predictio
    Leslie A Lenert; Fiscal Year: 2013
    ..in an elastic cloud environment: 1) use of temporal alignment of critical events including use of gene sequence alignment methods to relax requirements for exact temporal matching;and, 2) use of conceptual distance metrics to ..
  17. Basonuclin and Ribosome Biogenesis in Mouse Oocyte and Embryo
    Richard M Schultz; Fiscal Year: 2010
    ..e., cytoplasmically expressed region) of each v-rDNA. Using multiple sequence alignment, this investigation will determine if variable regions (markers) exist among rRNAs, which indicate rRNA ..
  18. Computational methods for structural-functional studies of proteins
    Nick V Grishin; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Accurate multiple sequence alignment (MSA) is the major unsolved problem in protein bioinformatics...
  19. Adapting Phred/Phrap/Consed for NextGen Sequencing
    PHILIP P GREEN; Fiscal Year: 2012
    ..We will further improve cross_match (the flexible sequence alignment program which is part of phred/phrap/consed) and our new ultrafast aligner phaster for mapping large numbers ..
  20. FPGA-based High Performance Computing
    MARTIN HERBORDT; Fiscal Year: 2009
    ..creating FGPA-accelerated versions of production applications from three key domains: molecular dynamics, sequence alignment, and docking...
  21. CODEHOP: Unique web-based technology for gene discovery
    TIMOTHY ROSE; Fiscal Year: 2009
    ..Unlike the "Basic Local Sequence Alignment Tool (BLAST) used to detect related sequences in silico, CODEHOPs can search for related sequences in the ..
  22. New algorithms and tools for large-scale genomic analyses
    Aaron R Quinlan; Fiscal Year: 2013
    ..g., a gene, sequence alignment, ChIP-seq peak, or anything that can be described with chromosome coordinates)...
  23. AlignShop: a comprehensive multiple sequence alignment editor and analysis tool
    Luke E Ulrich; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Multiple sequence alignment (MSA) is a core element of bioinformatics, comparative genomics, phylogenetics, molecular, and structural biology...
  24. Lysine Biosynthesis in Yeast
    Paul Cook; Fiscal Year: 2007
    ..Additionally, possible catalytic and binding residues in the homocitrate synthase have been identified by multiple sequence alignment, and alanine scanning mutagenesis will be applied to these. [unreadable] [unreadable]
  25. Genetics of Ocular Adenoviruses
    James Chodosh; Fiscal Year: 2006
    ..D adenoviruses for differences in nucleotide and predicted amino acid sequences will be performed using sequence alignment and analysis software, and are expected to reveal potential pathogenesis traits for future study...
  26. Enzymology of Homoserine Acylation in Methionine Biosynt
    TIMOTHY BORN; Fiscal Year: 2003
    ..This will be accomplished through a combination of sequence alignment, site-directed mutagenesis, chemical modification, and steady-state kinetic characterization...
  27. THE BACTEROIDES FORSYTHUS GENOME PROJECT
    Steven Gill; Fiscal Year: 2001
    ..Gene identification is enhanced by utilizing tools for multiple sequence alignment allowing us to build both orthologous and paralogous gene families...
  28. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2010
    ..A novel statistical model for nucleosorne DNA sequence alignment was proposed in the preliminary study...
  29. MULTIPLE REPRESENTATIONS OF BIOLOGICAL SEQUENCES
    Douglas Brutlag; Fiscal Year: 1999
    ..structure, 5) compare the prediction of protein secondary structure with existing method 6) build a near-optimal sequence alignment workbench, and 7) predict structured and unstructured regions in proteins from near- optimal alignments.
  30. ANALYSIS OF RETINAL DEGENERATION IN DROSOPHILA
    Ivana Delalle; Fiscal Year: 2005
    ..Once the genes have been cloned, mammalian hornologues will be searched for using sequence alignment methodologies. The mentor's laboratory has screened the autosomes for mutations of this nature...
  31. STRUCTURAL AND DYNAMIC STUDY OF MODEL HEME COMPLEXES
    GERD LA MAR; Fiscal Year: 2004
    ..characterize equilibrium intermediates in the thermal denaturation of Aplysia Mb, characterize the sequence alignment, folding topology and identify distal residues in a series of "mini" or "compact" (109-118 residue) globins, ..
  32. MULTISPECTRAL BACTERIAL IDENTIFICATION
    STEVEN ROBLES; Fiscal Year: 2002
    ..to couple this new multispectral technology to existing identification technologies that utilize 16S rRNA sequence alignment. Using this integrated identification protocol, bacteria that may be associated with chronic conditions (e.g...
  33. NMR OF TRINUCLEOTIDE REPEATS--NEURODEGENERATIVE DISEASE
    Xiaolian Gao; Fiscal Year: 1999
    ..The specific aims include: 1) Characterization of the sequence alignment and helical conformation of the GAA and TTC TR sequences and the variations of these properties as a ..
  34. Error Correction in Multiple Sequence Alignments
    Dan Graur; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Global multiple sequence alignment is the most basic step in the comparative study of molecular sequences...
  35. Universal Fingerprinting Chips
    Kenneth Beattie; Fiscal Year: 2006
    ..Phylogenetic trees constructed using Amerigenics' UFCtree software will be compared with those obtained by the traditional sequence alignment method. [unreadable] [unreadable] [unreadable]
  36. Siderophore transport mechanism via membrane receptors
    Ranjan Chakraborty; Fiscal Year: 2004
    ..This will be done by: 1. Identification of the conserved regions through multiple sequence alignment of the 19-receptor proteins transporting ferric siderophores...
  37. Improve homology modeling for membrane proteins by conserved inter-residue intera
    Zhijun Li; Fiscal Year: 2009
    ..that the conserved interactions across homologous protein structures can be identified from a multiple sequence alignment of homologous proteins with >35% sequence identity, as that alignment can be obtained with high accuracy;(..
  38. MECHANISM OF ENZYME INHIBITION BY PHARMACOLOGICAL AGENTS
    John Colicelli; Fiscal Year: 1999
    ..b>Sequence alignment of different PDE types shows some conservation that is likely to reflect requirements for catalytic activity...
  39. Alignments and Improved Refinements for High-Accuracy Protein Structure Modeling
    Patrice Koehl; Fiscal Year: 2009
    ..2) Build high accuracy models for the target protein. Homology modeling based on a given sequence alignment between a target sequence and the sequence of a template protein whose structure is known usually involve ..
  40. Physics-Based Refinement of Comparative Protein Models
    Matthew Jacobson; Fiscal Year: 2009
    ..Two key features of this approach are that it should: (a) tolerate sequence alignment errors, and (b) provide models for large insertions, which are not aligned to template residues...
  41. Acetate and ATP binding in acetyl-CoA synthetase
    Kerry Smith; Fiscal Year: 2004
    ..Analysis of the S. enterica structure and sequence alignment between AMP-ACSs and the very closely related to the propionyl-CoA synthetases, which utilize propionate as ..
  42. Effect of Sequence Alignment Fidelity on Genome Research
    Michael Rosenberg; Fiscal Year: 2006
    ..For many complex, high-throughput genomic analyses, sequence alignment is among the very first steps...
  43. COMPREHENSIVE SEQUENCE ASSEMBLY ALGORITHM
    RONALD LUNDSTROM; Fiscal Year: 1993
    ..such as sensitive overlap detection, robust detection of sequencing errors, and multiple sequence alignment. In addition, we plan the following enhancements: l) We will employ a conservative assembly protocol which ..
  44. COMPUTATIONAL & LABORATORY STUDY OF P16/INK4 MUTATIONS
    Marc Greenblatt; Fiscal Year: 2004
    ..on genes associated with human diseases, but preliminary data indicate they can improve upon simple sequence alignment in predicting function...
  45. High-Accuracy Modeling for Remote Homologues of Known Structures
    Roberto Sanchez; Fiscal Year: 2009
    ..Model accuracy is influenced by the target-template sequence alignment accuracy and the structural similarity between target and template...
  46. COMPUTATIONAL & LABORATORY STUDY OF P16/INK4 MUTATIONS
    Marc Greenblatt; Fiscal Year: 2002
    ..on genes associated with human diseases, but preliminary data indicate they can improve upon simple sequence alignment in predicting function...
  47. Joint Center for Molecular Modeling
    Adam Godzik; Fiscal Year: 2009
    ..The same tools recently also provided a major breakthrough in multiple sequence alignment. Here we propose to apply these tools to protein structure analysis and use the resulting insights into ..
  48. High-throughput phylogenomic analysis of animal proteins
    Kimmen Sjolander; Fiscal Year: 2007
    ..For each group, a multiple sequence alignment, phylogenetic tree, and subfamily classifications will be produced...
  49. Sequencing, assembly and annotation of a second Drosoph*
    Richard Gibbs; Fiscal Year: 2002
    ..pseudoobscura genes are fully represented. Two innovations for computer analysis of large sequence data sets will be explored. The per read cost for this work will be less than $1.80. ..
  50. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 1999
    ..Finally, we will explore other sequence alignment problems that may be synergistically related to our genomic alignment research.
  51. OPTIMIZED PROTEIN INFORMATICS
    Shalom Rackovsky; Fiscal Year: 2007
    ..The specific thrust of this work is the development of new approaches to sequence alignment and homology searching.
  52. Computational Approach to Ligand Discovery for LPA GPCR and PPAR
    Abby L Parrill; Fiscal Year: 2010
    ..This research can therefore lead to new treatments for cardiovascular disease and cancer. ..
  53. A DNA SEQUENCE ASSEMBLY PROGRAM
    Xiaoqiu Huang; Fiscal Year: 2003
    ..The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers. ..
  54. Mark I Model 68A Rodent/Cell line Gamma Irradiator
    Sanford Feldman; Fiscal Year: 2004
    ....
  55. The toxin-antitoxin system of Staphylococcus aureus.
    AMBROSE LIN YAU CHEUNG; Fiscal Year: 2010
    ..As therapy options against multidrug resistant S. aureus are limited, our screening assays will provide the initial compounds against MazE for the development of novel antimicrobial therapy against S. aureus ..
  56. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2006
    ..for computational sequence analysis, and motivate approaches substantially different from standard primary sequence alignment methods...
  57. Binding and regulation mechanism for S aureus
    Ambrose Cheung; Fiscal Year: 2006
    ..An understanding of these mechanisms will facilitate the development of novel agents that interfere with the function of the SarA family and the ensuing synthesis of cell wall adhesins and toxins. ..
  58. Sequence alignment fidelity in genomics and bioinformatics
    Michael S Rosenberg; Fiscal Year: 2010
    ..For many complex, high-throughput analyses of genome data, sequence alignment is among the very first steps...
  59. Characterization of sar-agr Interactions in S. aureus
    AMBROSE LIN YAU CHEUNG; Fiscal Year: 2010
    ..Our goal is to understand how SarA controls target gene and how other intracellular regulators affect SarA expression in S. aureus. ..
  60. Rat, a regulator of autolysis in S. aureus
    Ambrose Cheung; Fiscal Year: 2008
    ..Our long-term goal is to promote autolysis with an anti-Rat or pro-SarV strategy without developing an untoward impact on virulence. ..
  61. IN VIVO GENE EXPRESSION IN STAPHYLOCCUS AUREUS
    Ambrose Cheung; Fiscal Year: 2009
    ..Upon the completion of these studies, we hope to understand how sae is activated in vivo and what target genes sae impacts during infection. ..
  62. Re-engineering the MEGA software package
    Sudhir Kumar; Fiscal Year: 2009
    ..These core software enhancements will contribute to the longevity of MEGA for use in molecular evolution, bioinformatics, functional genomics, computational biology, and basic biomedicine applications. ..