S F Altschul

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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

Detail Information

Publications19

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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. ncbi 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...
  8. ncbi 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
    ..Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database...
  9. ncbi 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...
  10. ncbi 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
  11. ncbi 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...
  12. ncbi The effectiveness of position- and composition-specific gap costs for protein similarity searches
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:i15-23. 2008
    ....
  13. ncbi 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
    ..ncbi.nih.gov/pub/SALTO/), and has been incorporated to Cn3D structure/alignment viewer. CONTACT: ...
  14. ncbi 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)...
  15. ncbi 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...
  16. ncbi 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
    ....
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...