Mulan: multiple-sequence alignment to predict functional elements in genomic sequences

Abstract

Multiple sequence alignment analysis is a powerful approach for translating the evolutionary selective power into phylogenetic relationships to localize functional coding and noncoding genomic elements. The tool Mulan (http://mulan.dcode.org/) has been designed to effectively perform multiple comparisons of genomic sequences necessary to facilitate bioinformatic-driven biological discoveries. The Mulan network server is capable of comparing both closely and distantly related genomes to identify conserved elements over a broad range of evolutionary time. Several novel algorithms are brought together in this tool: the tba multisequence aligner program used to rapidly identify local sequence conservation and the multiTF program to detect evolutionarily conserved transcription factor binding sites in alignments. Mulan is integrated with the ERC Browser, the UCSC Genome Browser for quick uploads of available sequences and supports two-way communication with the GALA database to overlay GALA functional genome annotation with sequence conservation profiles. Local multiple alignments computed by Mulan ensure reliable representation of short- and large-scale genomic rearrangements in distant organisms. Recently, we have also introduced the ability to handle duplications to permit the reliable reconstruction of evolutionary events that underlie the genome sequence data. Here, we describe the main features of the Mulan tool that include the interactive modification of critical conservation parameters, visualization options, and dynamic access to sequence data from visual graphs for flexible and easy-to-perform analysis of differentially evolving genomic regions.

Fig. 1

Accessing the Mulan tool from the homepage at http://mulan.dcode.org (A) or from the ECR Browser “Synteny/Alignments” link (B).

Fig. 2

Each sequence can be pasted in, in FASTA format, uploaded as a FASTA file, or entered as an accession number along with the available annotation (A). Alternatively, sequences can be fetched from the UCSC Genome Browser individually using the “Upload” function (A), or in groups (Batch Upload System) Browser (B). Once sequences have been uploaded, the program acknowledges the receipt (C).

Fig. 3

Mulan defines a guiding phylogenetic tree before proceeding with the detailed sequence alignment. The user has the option to submit modifications to this tree.

Fig. 4

A completed alignment request results in a “summary page” that provides links to the interactive visualization platform, pairwise dynamic plots, dot plots, annotation files, sequence files, and a portal to the transcription factor binding site analysis software, MultiTF.

Fig. 5

Mulan interactive alignment customization options (A) and graphical display of alignments (B).

Fig. 6

Contig ordering based on homology to the reference sequence. The top layer of shaded lines indicates the location of contigs from a second sequence aligned to the base sequence where right-turned triangles specify forward strand alignments, and left-turned triangles correspond to reverse strand alignments.

Fig. 7

Mulan alignment analysis options: color density by interspecies conservation (A) and summary of conservation display (B).

Fig. 8

MultiTF portal available from Mulan “summary page.” First menu allows users to define the types of transcription factor binding site matrices to be used in the analysis, along with similarity thresholds (A). Next, the user selects either all or a subset of available transcription factors from the TRANSFAC library (B). Results are provided on an interactive summary page.

Fig. 9

Transcription factor binding sites can be juxtaposed on the Mulan multiple alignment graphics and several clustering and visualization options are provided for customized analysis (A). Similarly, the binding sites can be visualized within the textual alignment (B).