S F Altschul

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases
    S F Altschul
    NCBI, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Trends Biochem Sci 23:444-7. 1998
  2. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
  3. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
  4. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
  5. 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
  6. ncbi request reprint Generalized affine gap costs for protein sequence alignment
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 32:88-96. 1998
  7. pmc PSI-BLAST pseudocounts and the minimum description length principle
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 37:815-24. 2009
  8. pmc The construction and use of log-odds substitution scores for multiple sequence alignment
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 6:e1000852. 2010
  9. pmc The estimation of statistical parameters for local alignment score distributions
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:351-61. 2001
  10. ncbi request reprint IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    A A Schaffer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 15:1000-11. 1999

Detail Information

Publications22

  1. ncbi request reprint Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases
    S F Altschul
    NCBI, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Trends Biochem Sci 23:444-7. 1998
  2. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
    ....
  3. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
    ..Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server...
  4. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
    ..In a typical database search, at least one of these criteria is satisfied by over half the related sequence pairs. Compositional substitution matrix adjustment is now available in NCBI's protein-protein version of blast...
  5. 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...
  6. ncbi request reprint Generalized affine gap costs for protein sequence alignment
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 32:88-96. 1998
    ..Guidelines for selecting generalized affine gap costs are discussed, as is their possible application to multiple alignment...
  7. pmc PSI-BLAST pseudocounts and the minimum description length principle
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 37:815-24. 2009
    ..A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default...
  8. pmc The construction and use of log-odds substitution scores for multiple sequence alignment
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 6:e1000852. 2010
    ..We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum...
  9. pmc The estimation of statistical parameters for local alignment score distributions
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:351-61. 2001
    ..We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects...
  10. ncbi request reprint IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    A A Schaffer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 15:1000-11. 1999
    ..One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST)...
  11. pmc Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    A A Schaffer
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:2994-3005. 2001
    ..The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST...
  12. ncbi request reprint Local alignment statistics
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Methods Enzymol 266:460-80. 1996
  13. ncbi request reprint Basic local alignment search tool
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
    J Mol Biol 215:403-10. 1990
    ..In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity...
  14. ncbi request reprint The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:902-11. 2005
    ..RESULTS: This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices...
  15. pmc Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
    Robert L Strausberg
    National Cancer Institute, Bethessda, MD 20892 2580, USA
    Proc Natl Acad Sci U S A 99:16899-903. 2002
    ..All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov)...
  16. ncbi request reprint A structure-based method for protein sequence alignment
    Maricel G Kann
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
    Bioinformatics 21:1451-6. 2005
    ....
  17. pmc The effectiveness of position- and composition-specific gap costs for protein similarity searches
    Aleksandar Stojmirovińá
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:i15-23. 2008
    ....
  18. pmc Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:5966-73. 2006
    ..A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set...
  19. pmc Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
    Protein Sci 3:2045-54. 1994
    ..The GST domain is a widespread, conserved enzymatic module that may be covalently or noncovalently complexed with other proteins. Regulation of protein assembly and folding may be 1 of the functions of GST...
  20. pmc SAGEmap: a public gene expression resource
    A E Lash
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894 USA
    Genome Res 10:1051-60. 2000
    ....
  21. pmc The compositional adjustment of amino acid substitution matrices
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 100:15688-93. 2003
    ..Composition-specific substitution matrix adjustment is shown to be of utility for comparing compositionally biased proteins, including those of organisms with nucleotide-biased, and therefore codon-biased, genomes or isochores...
  22. pmc Characterization of gene expression in resting and activated mast cells
    H Chen
    Arthritis and Rheumatism Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Exp Med 188:1657-68. 1998
    ..Significantly, the majority of genes differentially expressed in this well-studied model of mast cell activation have not been identified before this analysis...