MetWAMer: eukaryotic translation initiation site prediction

Clicks: 159
ID: 82302
2008
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Abstract

Abstract

Background

Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.

Results

MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.

Conclusion

We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

Reference Key
volker2008metwamerbmc Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Volker, Brendel;E, Sparks Michael;
Journal BMC Bioinformatics
Year 2008
DOI
DOI not found
URL
http://www.biomedcentral.com/1471-2105/9/381
Keywords
Biology (General) Medicine Materials of engineering and construction. Mechanics of materials Electrical engineering. Electronics. Nuclear engineering Computer applications to medicine. Medical informatics environmental sciences education (general) management. industrial management special aspects of education computer engineering. computer hardware electronic computers. computer science

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