leicray

The DBASS databases are a total mess. It's useful that they have attempted to record splice sites created by sequence variants, but their variant description system is so far removed...

I was following the discussion (and agreeing entirely with your thoughts on the matter) until I got to the phrase "...should _not_ support partial transcripts...". Should this say "...partial alignments..."?...

I cannot see any way forward here because NCBI does not provide alignment information for mapping NM_006060.x onto GRCh37.

Thanks for the reply. I am still waiting to hear back from the sysop who built exonerate for the system that I am using. I will give him a nudge...

exonerate has been rebuilt from the master branch and selenocysteine is now being handled correctly. However, when I align the transcript CDS with the protein sequence for the SELENON gene,...

Have you had time to debug the numbering issue yet?

Exonerate was written to be used in an analysis pipeline and output to `stdout` was something of an afterthought. This was confirmed to me many years ago by Ewan Birney...