Putative Novel Alternative
Splicing Variants (PuNAS)
Our novel algorithm was used to compare EST queries based on known alternative splicing transcripts
using EST known transcript-genomic sequence alignment. (Lim et al., unpublished data).
TIGR gene indices include alternative splicing variants identified from a given 529,525 ESTs and 25,660 expressed transcripts (ETs).
Only the sequence with the best BLAST alignment of similarity against the known alternative splicing (AS) sequence was retained.
If the best-hit alignment was collinear, it was regarded to be an alternative splicing event.
If the best-hit alignment contained an insertion (Figure A) or deletion (Figure B) of an EST query, we assumed it to be an alternative splicing form never seen before, at least in the current AS database; the insertion and deletion events were indicated as case 1 and case 2, respectively. The novel alternative splicing events were validated using BLAT sequence similarity searches against genomic sequences. This was followed by checking the alignment between the case region and genomic sequences using BLAT, confirming the exon-intron boundary (we allowed the AG/GT, AG/GC, and GC/AG intron types), noting the intron phases, and validating the translation of alternative splicing.