Hi I would do it programmatically. You do not even need to know much of PERL to create your own simple scripts and the ENSEMBL APIs.
Go to http://www.ensembl.org and look for the APIs in the Docs & FAQ's section. It is full of instructions and examples. Good luck Pedro -- Pedro Fernandes Centro Português de Bioinformática Instituto Gulbenkian de Ciência Apartado 14 2781 OEIRAS PORTUGAL -------------------------------------- Quoting dale richardson <[email protected]>: > Hello All, > > Please forgive me if this post comes off as inexperienced, but if any > of you have the time I would like to hear your suggestions on the > following problem. > > I've got a set of genomic DNA sequences for a number of species. What > I want to do is to obtain only full-length cDNA matches to these > genomic sequences from GenBank, excluding Refseq sequences. What I've > been doing so far is blasting these genomic sequences against the nr > nucleotide database and manually evaluating which hits to keep or > discard, depending on the coverage of the subject sequence to the > query. While this method may be suitable for organisms with poorly > characterized expression data, when trying to do this for mouse or > human the task becomes entirely daunting. > > So my question is this: > > What is the most efficient way to obtain a set of cDNA sequences that > match to a set of genomic DNA sequences while excluding spurious > hits , RefSeq sequences and "pseudo" full length cDNAs? > > As you can imagine, I am interesting in looking for alternative splice > variants for a number of genes. > > Any information or help that you could graciously muster would be very > much appreciated. > > with sincere regards, > > dale richardson > > > > > > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
