The construction and use of log-odds substitution scores for multiple sequence alignment.

PLoS Computational Biology
Stephen F AltschulYi-Kuo Yu

Abstract

Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct "BILD" ("Bayesian Integral Log-odds") substitution scores from prior distributions describing columns of related letters. This approach has been used previously only to define scores for aligning individual sequences to sequence profiles, but it has much broader applicability. We describe how to calculate BILD scores efficiently, and illustrate their uses in Gibbs sampling optimization procedures, gapped alignment, and the construction of hidden Markov model profiles. BILD scores enable automated selection of optimal motif and domain model widths, and can inform the decision of whether to include a sequence in a multiple alignment, and the selection of insertion and deletion locations. Other applications include the classification of related sequences into subfamilies, and the definition of profile-profile alignment scores. Although a fully realized...Continue Reading

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Citations

May 16, 2014·Bioinformatics·Walyd KhenoussiJulie D Thompson
Dec 7, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xugang YeStephen F Altschul
May 11, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Lu MengMichael S Waterman
Jun 28, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xugang YeStephen F Altschul
Jun 28, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yi-Kuo Yu, Stephen F Altschul
Oct 15, 2011·Bioinformatics·Xugang YeStephen F Altschul
Sep 18, 2013·BMC Evolutionary Biology·Shijun ChengDaniel R Gallie
Jan 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Viet-An NguyenStephen F Altschul
Apr 5, 2011·Current Opinion in Structural Biology·Johannes Söding, Michael Remmert
May 23, 2012·Comparative and Functional Genomics·Ryan M Patrick, Karen S Browning
Oct 26, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shuai Cheng LiMing Li
Dec 4, 2010·Molecular and Biochemical Parasitology·Heather J PainterManuel Llinás
Apr 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Joshua B RadkeMichael W White
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May 3, 2018·PLoS Pathogens·Joshua B RadkeMichael W White
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Mar 3, 2017·MSphere·Dong-Pyo HongMichael W White
Oct 9, 2014·Bioinformatics·Yi-Kuo YuStephen F Altschul
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Nov 18, 2015·PLoS Computational Biology·Alejandro OchoaMona Singh
May 19, 2016·PLoS Computational Biology·Andrew F Neuwald, Stephen F Altschul
Jul 9, 2016·BMC Bioinformatics·Renaud VanhoutreveJulie D Thompson
Dec 22, 2016·PLoS Computational Biology·Andrew F Neuwald, Stephen F Altschul
Jun 6, 2018·PeerJ·Adam L BazinetShashikala Ratnayake
Nov 5, 2019·Frontiers in Genetics·Nidhi ShahMihai Pop

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Software Mentioned

HMMsearch
ClustalW
HMMcalibrate
PlasmoDB
BLAST
COBALT
ProbCons
Rose
Rose program
Linux

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