Robert C Edgar

Summary

Publications

  1. ncbi request reprint SATCHMO: sequence alignment and tree construction using hidden Markov models
    Robert C Edgar
    195 Roque Moraes Drive, Mill Valley, CA 94941, USA
    Bioinformatics 19:1404-11. 2003
  2. pmc Optimizing substitution matrix choice and gap parameters for sequence alignment
    Robert C Edgar
    BMC Bioinformatics 10:396. 2009
  3. pmc Quality measures for protein alignment benchmarks
    Robert C Edgar
    Nucleic Acids Res 38:2145-53. 2010
  4. pmc PILER-CR: fast and accurate identification of CRISPR repeats
    Robert C Edgar
    BMC Bioinformatics 8:18. 2007
  5. ncbi request reprint Multiple sequence alignment
    Robert C Edgar
    Curr Opin Struct Biol 16:368-73. 2006
  6. ncbi request reprint PILER: identification and classification of genomic repeats
    Robert C Edgar
    Bioinformatics 21:i152-8. 2005
  7. 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
  8. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
  9. ncbi request reprint COACH: profile-profile alignment of protein families using hidden Markov models
    Robert C Edgar
    Bioinformatics 20:1309-18. 2004
  10. ncbi request reprint A comparison of scoring functions for protein sequence profile alignment
    Robert C Edgar
    Bioinformatics 20:1301-8. 2004

Detail Information

Publications16

  1. ncbi request reprint SATCHMO: sequence alignment and tree construction using hidden Markov models
    Robert 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...
  2. pmc 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...
  3. pmc Quality measures for protein alignment benchmarks
    Robert 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...
  4. pmc 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...
  5. ncbi request reprint 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...
  6. ncbi request reprint PILER: identification and classification of genomic repeats
    Robert C Edgar
    Bioinformatics 21:i152-8. 2005
    ..We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster...
  7. 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...
  8. 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...
  9. ncbi request reprint 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...
  10. ncbi request reprint 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...
  11. pmc Local homology recognition and distance measures in linear time using compressed amino acid alphabets
    Robert C Edgar
    Nucleic Acids Res 32:380-5. 2004
    ....
  12. doi request reprint Search and clustering orders of magnitude faster than BLAST
    Robert 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...
  13. pmc 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...
  14. pmc 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...
  15. pmc 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
    ....
  16. ncbi request reprint 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...