Hi ,
I want to know if anyone is familar with searcing for alternave proteins.I have identified new transcripts of a known gene and want to compare the resulting alternative proteins with existing alternative or related proteins in other spicies. One of my transcripts splices out exon 4. The problem is that if I run a pBlast on the alternative protein, the program devides my query seq so that I get an alignment of the protein seq which corresponds to E1-E3 and one which corresponds to E5-E6. It doesnt show the in between alignment but still the score is 100% if the rest of my seq match. How can I get pBlast to do an entire seq alignment? Maybe other ideas?
:)

One way to go about it would be to use global alignment instead of local alignment. Blast is a local alignment (that's what the L stands for) and so prefers to break alignments up when the quality drops off. You should try to use a global aligner such as FASTA or a multiple sequence aligner (clustalw/clustalx). If you want to get all known splice variants of your protein in different species then ENSEMBL is probably a good place to start. What organisms are you working in by the way, as this may affect where you go for sequences.

Cheers,

Ryan