How sensitive is BLAST to detecting the various events that lead to isoforms of transcripts. I've had decent success in being able to capture orthologs things like nonsense mediated decay or highly truncated transcripts. However for more subtle differences or alternative splices, I am concerned that BLAST might not be sensitive enough to differentiate strongly between the two.
My concern comes from the idea of a BLAST hit, two transcripts could be identical up to a given point. BLAST could generate hits against the same regions that score the same or close enough to impact the selection of the best hit. What is also a concern is in truncations or alternative splices, where BLAST might not capture the order of splicing, making two very different transcripts appear to be almost identical.
Is BLAST sufficient for detecting orthologs of transcript isoforms, or is it going to be unreliable? I was wondering if it would be worth repeating a similar analysis but using Needleman-Wunsch to handle the alignments and scoring. The computational cost is much larger, but it might be better able to handle more conserved transcript isoforms.
EDIT: My end goal is to map orthologous transcripts of genes to sequences found in my de novo RNA-Seq data. In other words, I want to go a level deeper and not just map my RNA-Seq data to genes, but annotate for transcripts as well.