MetWAMer: eukaryotic translation initiation site prediction.
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.


CONCLUSIONS
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.
Sparks
Michael E
ME
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA. mespar1@iastate.edu
Brendel
Volker
V
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D001499:Bayes Theorem; D018387:Codon, Initiator; D019295:Computational Biology; D005057:Eukaryotic Cells / Q000378:metabolism*; D008390:Markov Chains; D015233:Models, Statistical; D016366:Open Reading Frames; D011237:Predictive Value of Tests; D014176:Protein Biosynthesis; D011499:Protein Processing, Post-Translational; D012333:RNA, Messenger / Q000378:metabolism; D012372:ROC Curve; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D018387:Codon, Initiator; D012333:RNA, Messenger
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