MOTIVATION: mRNA sequences and expressed sequence tags represent some of the 
most abundant experimental data for identifying genes and alternatively spliced 
products in metazoans. These transcript sequences are frequently studied by 
aligning them to a genomic sequence template. For existing programs, 
error-prone, polymorphic and cross-species data, as well as non-canonical splice 
sites, still present significant barriers to producing accurate, complete 
alignments.
RESULTS: We took a novel approach to spliced alignment that meaningfully 
combined information from sequence similarity with that obtained from PSSM 
splice site models. Scoring systems were chosen to maximize their power of 
discrimination, and dynamic programming (DP) was employed to guarantee optimal 
solutions would be found. The resultant program, EXALIN, performed better than 
other popular tools tested under a wide range of conditions that included 
detection of micro-exons and human-mouse cross-species comparisons. For improved 
speed with only a marginal decrease in splice site prediction accuracy, EXALIN 
could perform limited DP guided by a result from BLASTN.
AVAILABILITY: The source code, binaries, scripts, scoring matrices and splice 
site models for human, mouse, rice and Caenorhabditis elegans utilized in this 
study are posted at http://blast.wustl.edu/exalin. The software (scripts, source 
code and binaries) is copyrighted but free for all to use.