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

Will Spooner whs at ebi.ac.uk
Fri Apr 22 08:31:19 EDT 2005

Hi Michael,

What you have is a Bio::Search::Result object generated from your blast 
report, and you would like to use this to generate a GFF file to load into 
LDAS? Whilst there is nothing like this in the Ensembl code, I do 
see a Bio::SearchIO::Writer::GbrowseGFF module that may suit your needs.

If you have blasted against the Ensembl cdna file but want the chromosome 
location of the alignments, then you can parse the blast report into 
EnsemblHSP/Hit/Result objects. These extend BioPerl's 
GenericHSP/Hit/Result to exactly this end, and can be implemented in the 
manner described by the SearchIO howto;
The code can be found in the 'modules' project of Ensembl's CVS 
repository (modules/Bio/Search/HSP/EnsemblHSP.pm etc).

All the best,


On Wed, 13 Apr 2005, Michael Seewald wrote:

> 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 )
> and
> 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
> Bioinformatics
> Bayer HealthCare AG
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