Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Ivan Ovcharenko, Gabriela G. Loots, Belinda M. Giardine, Minmei Hou, Jian Ma, Ross Cameron Hardison, Lisa Stubbs, Webb Miller

Research output: Contribution to journalArticle

181 Citations (Scopus)

Abstract

Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short- and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multispecies comparisons of the GATA3 gene focus and the identification of elements that are conserved in a different way in avians than in other genomes, allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx.psu.edu/miller∧b/.

Original languageEnglish (US)
Pages (from-to)184-194
Number of pages11
JournalGenome Research
Volume15
Issue number1
DOIs
StatePublished - Jan 1 2005

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Sequence Alignment
Genome
Transcription Factors
Binding Sites
Genes
Birds
Sequence Analysis
Vertebrates
Software
Communication
Databases

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Ovcharenko, I., Loots, G. G., Giardine, B. M., Hou, M., Ma, J., Hardison, R. C., ... Miller, W. (2005). Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Research, 15(1), 184-194. https://doi.org/10.1101/gr.3007205
Ovcharenko, Ivan ; Loots, Gabriela G. ; Giardine, Belinda M. ; Hou, Minmei ; Ma, Jian ; Hardison, Ross Cameron ; Stubbs, Lisa ; Miller, Webb. / Mulan : Multiple-sequence local alignment and visualization for studying function and evolution. In: Genome Research. 2005 ; Vol. 15, No. 1. pp. 184-194.
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Ovcharenko, I, Loots, GG, Giardine, BM, Hou, M, Ma, J, Hardison, RC, Stubbs, L & Miller, W 2005, 'Mulan: Multiple-sequence local alignment and visualization for studying function and evolution', Genome Research, vol. 15, no. 1, pp. 184-194. https://doi.org/10.1101/gr.3007205

Mulan : Multiple-sequence local alignment and visualization for studying function and evolution. / Ovcharenko, Ivan; Loots, Gabriela G.; Giardine, Belinda M.; Hou, Minmei; Ma, Jian; Hardison, Ross Cameron; Stubbs, Lisa; Miller, Webb.

In: Genome Research, Vol. 15, No. 1, 01.01.2005, p. 184-194.

Research output: Contribution to journalArticle

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