[BiO BB] Efficient way to retrieve full length cDNA sequences from GenBank?

Pedro Fernandes pfern at igc.gulbenkian.pt
Thu Apr 2 11:41:51 EDT 2009


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 <dalesan at gmail.com>:

> 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
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>




More information about the BBB mailing list