Dataset Information

Algorithms for locating extremely conserved elements in multiple sequence alignments.

ABSTRACT:

Background

In 2004, Bejerano et al. announced the startling discovery of hundreds of "ultraconserved elements", long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research.

Results

We generalize the notion of ultraconserved element in a natural way from extraordinary human-rodent conservation to extraordinary conservation over an arbitrary set of species. We call these "Extremely Conserved Elements". There is a linear time algorithm to find all such Extremely Conserved Elements in any multiple sequence alignment, provided that the conservation is required to be across all the aligned species. For the general case of conservation across an arbitrary subset of the aligned species, we show that the question of whether there exists an Extremely Conserved Element is NP-complete. We illustrate the linear time algorithm by cataloguing all 177 Extremely Conserved Elements in the currently available 44-vertebrate whole-genome alignment, and point out some of the characteristics of these elements.

Conclusions

The NP-completeness in the case of conservation across an arbitrary subset of the aligned species implies that it is unlikely an efficient algorithm exists for this general case. Despite this fact, for the interesting case of conservation across all or most of the aligned species, our algorithm is efficient enough to be practical. The 177 Extremely Conserved Elements that we catalog demonstrate many of the characteristics of the original ultraconserved elements of Bejerano et al.

SUBMITTER: Tseng HH

PROVIDER: S-EPMC2808710 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Publications

Algorithms for locating extremely conserved elements in multiple sequence alignments.

Tseng Huei-Hun E HH Tompa Martin M

BMC bioinformatics 20091218

<h4>Background</h4>In 2004, Bejerano et al. announced the startling discovery of hundreds of "ultraconserved elements", long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research.<h4>Results</h4>We generalize the notion of ultraconserved element in a natural way from extraordinary human-rodent conservation to extraordinary conservation over an arbitrary set of species. We call these "Extremely Conserved Elements". There ...[more]

PMID: 20021665

Similar Datasets

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

Algorithms for locating extremely conserved elements in multiple sequence alignments.

Background

Results

Conclusions

Publications

Algorithms for locating extremely conserved elements in multiple sequence alignments.

Similar Datasets

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