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

[Martin MOKREJŠ]

Hi Dale,
  forget about GenBank, go for http://h-invitational.jp/ which collected
the full length cDNA data for you already.
martin

dale richardson wrote:
> 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


-- 
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
tel: +420-2-2195 1716
http://www.iresite.org
http://www.iresite.org/~mmokrejs