PicXAA is a probabilistic nonprogressive alignment algorithm that finds protein (or DNA) multiple sequence alignments with maximum expected accuracy. PicXAA greedily builds up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures the local similarities across sequences. PicXAA constantly yields accurate alignment results on a wide range of reference sets that have different characteristics, with especially remarkable improvements over other leading algorithms on sequence sets with high local similarities. In this chapter, we describe the overall alignment strategy used in PicXAA and discuss several important considerations for effective deployment of the algorithm.
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast statistical alignment. PLoS Comput Biol 5:e1000392PubMedCrossRefGoogle Scholar
Sahraeian SM, Yoon BJ (2010) PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple Sequences. Nucleic Acids Res 38:4917–4928PubMedCrossRefGoogle Scholar
Roshan U, Livesay DR (2006) Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22:2715–2721PubMedCrossRefGoogle Scholar
Gonnet GH, Cohen MA, Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256:1443–1445PubMedCrossRefGoogle Scholar
Sahraeian SM, Yoon BJ (2010) PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics 11(Suppl 1):S38CrossRefGoogle Scholar
Sahraeian SM, Yoon BJ (2011) PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. Nucleic Acids Res 39:W8–W12PubMedCrossRefGoogle Scholar