Where can I find transcriptome databases?
I'm doing local blast. I need to blast my fasta file against several cDNA databases but the ones I downloaded from Ensembl don't have gene names. Where can I find species specific cDNA/RNA databases with gene names in them to download?
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ENSEMBL Biomart : you can select the gene name and cDNA sequences. and of course the species
I want to download the entire trancriptome database which contains the sequences, gene name, ids, locations...
not just individual sequences.
You can download th whole cDNA sequences from any species in ensembl by specifying in biomart:
Thank you, NicoBxl. I think you are talking about the individual annotated genes in the genome while what I need is the entire "transcriptome" of a species so it is pointless for me to select "chromosome, gene start, gene end...".
Check this out this: http://www.ensembl.org/info/data/ftp/index.html. The "cDNA (FASTA)" databases are what I need but these databases contain almost everything but the gene names. I'm looking for similar files but contain gene names in them.