Computational methods for protein sequence analysis

Current Protocols in Protein Science
G Michaels, R Garian

Abstract

This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. A theoretical background for protein sequence analysis is provided first, followed by a discussion of matrix methods for sequence comparison (Matrix Methods for Sequence Comparison: Dot Plots). Sequence similarity searching is then presented, including the BLAST and FASTA databases. Other aspects of protein sequence analysis covered here are alignment methods, scoring matrices, multiple alignments, cluster methods and trees, and identification of functional sites.

References

Jul 1, 1992·Journal of Molecular Evolution·L AllisonC N Yee
Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·V BrendelS Karlin
Feb 1, 1992·Trends in Genetics : TIG·D J States
Jan 11, 1992·Nucleic Acids Research·E PizziC Saccone
Jan 1, 1991·Annual Review of Biophysics and Biophysical Chemistry·S KarlinS F Altschul
Feb 1, 1991·Computers and Biomedical Research, an International Journal·E C TylerP R Krause
Apr 25, 1991·Nucleic Acids Research·A Bairoch
Apr 1, 1990·Accident; Analysis and Prevention·J D States, D C Viano
Jan 1, 1990·Methods in Enzymology·W R Pearson
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 1, 1990·Methods in Enzymology·M GribskovD Eisenberg
Jan 1, 1990·Methods in Enzymology·M S Waterman, R Jones
Jan 1, 1990·Methods in Enzymology·D G GeorgeL T Hunt
Jan 1, 1990·Methods in Enzymology·P Argos, M Vingron
Jan 1, 1990·Methods in Enzymology·G J Barton
Jan 1, 1990·Methods in Enzymology·J F Collins, A F Coulson
Jan 1, 1990·Methods in Enzymology·G M LandauR Nussinov
Oct 20, 1987·Journal of Molecular Biology·M S Waterman, M Eggert
Jan 1, 1989·Protein Engineering·M KanaokaH Umeyama
Mar 22, 1985·Science·D J Lipman, W R Pearson
Jan 20, 1987·Journal of Molecular Biology·P Argos
May 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·M MurataJ L Sussman
Jan 15, 1974·Biochemistry·P Y Chou, G D Fasman
Mar 14, 1972·Journal of Molecular Biology·A D McLachlan
Oct 28, 1971·Journal of Molecular Biology·A D McLachlan
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Mar 1, 1966·Journal of Molecular Biology·W M Fitch
Jan 11, 1982·Nucleic Acids Research·J P Dumas, J Ninio
Feb 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·W J Wilbur, D J Lipman
Dec 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·J V Maizel, R P Lenk
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jan 1, 1981·Journal of Molecular Evolution·T F SmithW M Fitch
Jun 30, 1994·Journal of Biotechnology·S Pietrokovski
Apr 1, 1994·Journal of Pharmacokinetics and Biopharmaceutics·J R WadeN C Sambol
Sep 1, 1993·Proteins·S Henikoff, J G Henikoff
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M Rustici, A M Lesk

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Citations

Apr 4, 2017·Current Protocols in Protein Science·Jongchan WooSavithramma P Dinesh-Kumar
Apr 23, 2008·Current Protocols in Neuroscience·Elaine A Elion
Feb 12, 2008·Current Protocols in Molecular Biology·Elaine A Elion
Apr 3, 2016·Current Protocols in Molecular Biology·Chao-Kai ChouMien-Chie Hung
Apr 26, 2007·Clinical and Experimental Allergy : Journal of the British Society for Allergy and Clinical Immunology·R A McDermottS C Dreskin

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