[Bioperl-l] Help with parsing (BLAST/exonerate) for DAS server

Michael Seewald mseewald at gmail.com
Wed Apr 13 11:41:35 EDT 2005

Dear Bioperl developers,

I have posed the following questions already to the Ensembl helpdesk and the 
Ensembl-developers. Unfortunately, nobody could help me there (or was too 
busy..). I would really appreciate your help or any pointers to 
documentation/public examples.

I would like to set up a DAS server in order to add sequences (+their 
annotation) to the Ensembl ContigView. I have BLAST results of
1) short genomic sequences BLASTed vs. the chromosomes (
e.g.Homo_sapiens.NCBI35.nov.dna.chromosome.21.fa )
2) fragment transcript sequences (e.g. single Affy probes) BLASTed vs. 
Ensembl transcripts (e.g. Homo_sapiens.NCBI35.nov.cdna.fa).
Now, I would like to parse and format them into something that can be 
displayed using a DAS server like LDAS.

* Are there already scripts available that support the parsing of BLAST 
results and help to prepare them for the DAS server? Could you point me to 
the source (e.g. in the Ensembl source)?

* BLASTing versus the chromosomes and displaying sequences in the Contigview 
seems to be straightforward because the BLAST hits can be taken right away. 
What would you recommend, if I have transcript fragments, which could be the 
result of splicing? How can I properly deal with intron/exon boundaries? Is 
it a good idea to use Exonerate instead of BLAST here (or maybe in general 
for the alignment)?

Thanks & kind regards,
Michael Seewald

Dr. Michael Seewald
Bayer HealthCare AG

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