+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Exploratory analysis of multiple sequence alignments using phylogenies

Exploratory analysis of multiple sequence alignments using phylogenies

Computer Applications in the Biosciences 10(3): 243-247

The significance of an alignment between two sequences can be determined using well-known techniques but cannot be easily evaluated with multiple alignments due to the computational complexity. Therefore multiple alignment algorithms may produce an alignment between sequences even when they have little homology with other sequences. A program is presented that makes use of a phylogeny to explore the implications of an alignment. Using the phylogeny, branch lengths are inferred and a search is conducted for regions of unusually rapid or slow rates of change given the observed rates in the rest of the sequence. A very rapid rate of change can be due to either poor homology or due to rapid divergence because of selection. Phylogenies are calculated using either the neighbor joining algorithm of Saitou and Nei (Mol. Biol. Evol., 4, 406-425, 1987) or a phylogeny supplied by the user. The program also permits randomization of subsections of the sequences to determine the significance of the multiple alignment for these individual regions. The combination of these two simple methods permits rapid and interactive exploration of multiple sequence alignments.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 008654574

Download citation: RISBibTeXText

PMID: 7922679

DOI: 10.1093/bioinformatics/10.3.243

Related references

Exploratory visual analysis of conserved domains on multiple sequence alignments. Bmc Bioinformatics 10(Suppl. 11): S7, 2009

Advantages of using multiple sequence alignments over pairwise alignments when sequence similarity is low. Abstracts of Papers American Chemical Society 203(1-3): BIOL60, 1992

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments. Bmc Proceedings 8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica): S9, 2014

The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. Bioinformatics 35(1): 12-19, 2019

Building multiple sequence alignments with a flavor of HSSP alignments. Genetics and Molecular Research 5(1): 127-137, 2006

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56(4): 564-577, 2007

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments. Systematic Biology 56(4): 564-577, 2007

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. Journal of Molecular Biology 264(4): 823-838, 1996

Creation and analysis of protein multiple sequence alignments. Methods of Biochemical Analysis 43: 215-232, 2001

ESPript: Analysis of multiple sequence alignments in PostScript. Bioinformatics 15(4): 305-308, 1999

A comparative analysis of multiple sequence alignments for biological data. Bio-MedicalMaterialsandEngineering26Suppl1:S1781, 2015

Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. Genome Research 14(2): 313-318, 2004

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. Bmc Bioinformatics 13: 117, 2012

Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. Journal of Molecular Biology 307(3): 939-949, 2001

Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments. Bmc Bioinformatics 15: 157, 2014