Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

Journal Article · Wed Jul 14 04:00:00 EDT 2004 · Published in: Genome Research, vol. 15, no. 1, January 3, 2005, pp. 184-194

OSTI ID:15014479

Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

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 multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently 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://bio.cse.psu.edu/.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 15014479
• Report Number(s): UCRL-JRNL-205739
• Journal Information: Published in: Genome Research, vol. 15, no. 1, January 3, 2005, pp. 184-194, Journal Name: Published in: Genome Research, vol. 15, no. 1, January 3, 2005, pp. 184-194 Journal Issue: 1 Vol. 15
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ALGORITHMS
ALIGNMENT
BIRDS
COMMUNICATIONS
FUNCTIONALS
GENES
MODIFICATIONS
TRANSCRIPTION FACTORS
VERTEBRATES