Alternative Splicing And Transcript Diversity Databases

Question

[Pierre]

Hey guys,

EBI has this very nice database for fasta format sequences of all exons and transcripts. Unforuntanetely, these data are available currently only for human, mouse and rat.

I would like to have the same data for other species. Does anyone know if there are such databases - perhaps manually curated for a specific organism?

Thanks

Answer 1

[Malachi Griffith]

There are countless ways to obtain such information:

• From Ensembl you can get fasta files for many species from their FTP Download section. A GTF defining the structure of each transcript is also provided there.
• You can get FASTA sequences for each exon from Ensembl BioMart. Select database, then desired species, then under 'attributes' select 'sequences', expand the sequences section and then select 'exon sequences'. You can retrieve the result in fasta format.
• It is also possible to get exon sequences via the Ensembl API

• You could use the tool gffread from Cufflinks along with a GTF file and reference genome sequence to produce these files using a command like this:

  gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

• You could use the BEDTools utility fastaFromBed to produce these files. You would need a BED file of all exon coordinates. That could be obtained from the UCSC table browser among other options.

Choose your poison...

[Pierre]

Thanks a lot Malachi - I'll give a shot with BioMart.