SATCHMO: sequence alignment and tree construction using hidden Markov modelsRobert C Edgar
195 Roque Moraes Drive, Mill Valley, CA 94941, USA
Bioinformatics 19:1404-11. 2003
..SATCHMO generates profile hidden Markov models at each node; these are used to determine branching order, to align sequences and to predict structurally alignable regions...
Quality measures for protein alignment benchmarksRobert C Edgar
Nucleic Acids Res 38:2145-53. 2010
..A careful analysis of current protein multiple alignment benchmarks calls into question their ability to determine reliable algorithm rankings...
- Optimizing substitution matrix choice and gap parameters for sequence alignment
Robert C Edgar
BMC Bioinformatics 10:396. 2009
..Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments...
- PILER-CR: fast and accurate identification of CRISPR repeats
Robert C Edgar
BMC Bioinformatics 8:18. 2007
..However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output...
- Multiple sequence alignment
Robert C Edgar
Curr Opin Struct Biol 16:368-73. 2006
..Although CLUSTALW is still the most popular alignment tool to date, recent methods offer significantly better alignment quality and, in some cases, reduced computational cost...
- PILER: identification and classification of genomic repeats
Robert C Edgar
Bioinformatics 21:i152-8. 2005
..Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster. AVAILABILITY: The PILER software is freely available at http://www.drive5.com/piler...
- 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...
- 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...
- COACH: profile-profile alignment of protein families using hidden Markov models
Robert C Edgar
Bioinformatics 20:1309-18. 2004
..COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM...
- A comparison of scoring functions for protein sequence profile alignment
Robert C Edgar
Bioinformatics 20:1301-8. 2004
..Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence-sequence and sequence-profile methods, including BLAST and PSI-BLAST...
- Local homology recognition and distance measures in linear time using compressed amino acid alphabets
Robert C Edgar
Nucleic Acids Res 32:380-5. 2004
....
Search and clustering orders of magnitude faster than BLASTRobert C Edgar
Tiburon, CA 94920, USA
Bioinformatics 26:2460-1. 2010
..Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification...
- UCHIME improves sensitivity and speed of chimera detection
Robert C Edgar
Tiburon, CA, USA
Bioinformatics 27:2194-200. 2011
..Detection and removal of chimeras is therefore of critical importance in such experiments...
- Multiple alignment of protein sequences with repeats and rearrangements
Tu Minh Phuong
Department of Computer Science, Posts and Telecommunications Institute of Technology, Hanoi, Vietnam
Nucleic Acids Res 34:5932-42. 2006
..We conclude that ProDA is a practical tool for automated alignment of protein sequences with repeats and rearrangements in their domain architecture...
- Improved repeat identification and masking in Dipterans
Christopher D Smith
Department of Biology, San Francisco State University, San Francisco, CA, United States
Gene 389:1-9. 2007
....
- Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins
David La
Department of Chemistry, California State Polytechnic University at Pomona, 3801 West Temple Avenue, Pomona, California 91768, USA
Biochemistry 42:8988-98. 2003
..Additionally, we present amino acid composition data and average protein length comparisons for all 44 microbial genomes...
