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.