References:
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Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990)
Basic local alignment search tool
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Database homology search (BLAST)
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Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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Database homology search (PSI-BLAST)
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Stephen F. Altschul and Eugene V. Koonin (1998)
Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases
Trends Biochem. Sci. 23: 444-447
Database homology search (PSI-BLAST)
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Steven E. Brenner, Cyrus Chothia, and Tim J.P. Hubbard (1998)
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
Proc. Natl. Acad. Sci. USA 95: 6073-6078
Comparison of algorithms for pairwise sequence comparisons
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Jean-Michel Claverie (1993)
Detecting frame shifts by amino acid sequence comparison
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Original similarity matrix
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A model of evolutionary change in proteins
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Original similarity matrix
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D. Donnelly, J.P. Overington, S.V. Ruffle, J.H. Nugent, and T.L: Blundell (1993)
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Original similarity matrix
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Sean R. Eddy (1998)
Profile hidden Markov models
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Database homology search (HMM method)
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Steven Henikoff and Jorja G. Henikoff (1992)
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Original similarity matrix
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Steven Henikoff and Jorja G. Henikoff (1993)
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Comparison of similarity matrices
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Steven Henikoff and Jorja G. Henikoff (2000)
Amino acid substitution matrices
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Comparison of similarity matrices
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Mark S. Johnson and John P. Overington (1993)
A structural basis for sequence comparisons. An evaluation of scoring methodologies
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Original Ähnlichkeitsmatrix
Comparison of similarity matrices
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David T. Jones and Mark B. Swindells (2002)
Getting the most from PSI-BLAST
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Database homology search (PSI-BLAST)
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Jeffrey M. Koshi and Richard A. Goldstein (1997)
Mutation matrices and physical-chemical properties: correlations and implications
Proteins Struct. Funct. Genet. 27: 336-344
Comparison of similarity matrices
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Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, and David Haussler (1994)
Hidden Markov models in computational biology. Applications to protein modeling
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Database homology search (HMM method)
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W. Li, F. Pio, K. Pawlowski, and A. Godzik (2000)
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Database homology search (Saturated BLAST)
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David J. Lipman and William R. Pearson (1985)
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Database homology search (FASTP)
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A.C. May (1999)
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Comparison of similarity matrices
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P.C. Ng, J.G. Henikoff, and S. Henikoff (2000)
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Original similarity matrix
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William R. Pearson (1995)
Comparison of methods for searching protein sequence databases
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Comparison of similarity matrices
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William R. Pearson (1996)
Effective protein sequence comparison
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Primer to database searches
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William R. Pearson (1998)
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Database homology search: Calculation of significance
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William R. Pearson (2000)
Flexible sequence similarity searching with the FASTA3 program package
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Primer to database searches
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William R. Pearson and David J. Lipman (1988)
Improved tools for biological sequence comparison
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Database homology search (FASTA)
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William R. Pearson and Michael L. Sierk
The limits of protein sequence comparison?
Curr. Opin. Struct. Biol. 15: 254-260
Comparison of algorithms for pairwise sequence comparisons (Review)
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F. Plewniak, J.D. Thompson, and O. Poch (2000)
Ballast: blast post-processing based on locally conserved segments
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Database homology search (Ballast)
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Andreas Prlic, Francisco S. Domingues, and Manfred J. Sippl (2000)
Structure-derived substitution matrices for alignment of distantly related sequences
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Original similarity matrix
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Burkhard Rost (1999)
Twilight zone of protein sequence alignments
Protein Eng. 12: 85-94
Database homology search: Calculation of significance
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Alejandro A. Schäffer, L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001)
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
Nucleic Acids Res. 29: 2994-3005
Database homology search (PSI-BLAST)
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J.N. Selley, J. Swift, and T.K. Attwood (2001)
EASY - an Expert Analysis SYstem for interpreting database search outputs
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Database homology search (EASY)
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T.F. Smith and M.S. Waterman (1981)
Identification of common molecular sub-sequences
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Pairwise sequence comparison
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Rainer Spang and Martin Vingron (2001)
Limits of homology detection by pairwise sequence comparison
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Database homology search: Signifikanz-Berechnungen
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Kentaro Tomii and Minoru Kanehisa (1996)
Analysis of |