Where can I find transcriptome databases?

Question

[grayapply2009]

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?

[Nicolas Rosewick]

ENSEMBL Biomart : you can select the gene name and cDNA sequences. and of course the species

[grayapply2009]

I want to download the entire trancriptome database which contains the sequences, gene name, ids, locations...

not just individual sequences.

[Nicolas Rosewick]

You can download th whole cDNA sequences from any species in ensembl by specifying in biomart:

• Select ENSEMBL GENES
• The species you want
• In the left panel, you select Attributes
• Then select "Sequences" in the middle panel
• Open the SEQUENCES panel
• Select cDNA sequences
• Below in this page, open the HEADER panel and select Chromosome name, gene start, gene end, strand, etc... what you want
• Press to RESULTS (upper left button) and enjoy ;)

[grayapply2009]

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.

Answer 1

[dago]

Just today I read about the TSA and GEO on NCBI.

Maybe it can help.

Answer 2

[hugorody]

probably here you have everything you want

http://bioinformatics.psb.ugent.be/plaza/

or

http://www.phytozome.net/