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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
