Dataset Information

Exploratory visual analysis of conserved domains on multiple sequence alignments.

ABSTRACT: BACKGROUND: Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. This insight can be augmented by joint display of conserved domains along the sequences. By fusing this metadata visually, biologists can analyze sequence conservation and functional motifs simultaneously and efficiently. RESULTS: We present MSAVis, a new approach combining luminance and hue for simultaneous visualization of conserved motifs and sequence alignment. Input for the algorithm is a multiple sequence alignment in a standard format. The NCBI Conserved Domain Database (CDD) is used for finding conserved domains along the alignment. The visualization quickly identifies conserved domains, and allows both macro (sequence-long) and micro (small amino-acid neighborhood) views. CONCLUSION: MSAVis utilizes two visual cues, luminance and hue, to facilitate at-a-glance summary of the conservation of a user-provided protein alignment while enabling multiple comparisons among functional domains. These visual cues are preattentive and separable so that the relationship between conservation strength and domain membership can be understood. The MSAVis software, written in Python and using BioPython and OpenGL, can be found at http://agbase.msstate.edu/tools/MSAVis.html.

SUBMITTER: Jankun-Kelly TJ

PROVIDER: S-EPMC3226196 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Exploratory visual analysis of conserved domains on multiple sequence alignments.

Jankun-Kelly T J TJ Lindeman Andrew D AD Bridges Susan M SM

BMC bioinformatics 20091008

<h4>Background</h4>Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. This insight can be augmented by joint display of conserved domains along the sequences. By fusing this metadata visually, biologists can analyze sequence conservation and functional motifs simultaneously and efficiently.<h4>Results</h4>We present MSAVis, a new approach comb ...[more]

PMID: 19811691

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Project description:BACKGROUND:Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. RESULTS:AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". CONCLUSIONS:AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer.

Dataset Information

Exploratory visual analysis of conserved domains on multiple sequence alignments.

Publications

Exploratory visual analysis of conserved domains on multiple sequence alignments.

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