Where To Download Annotated Transcripts Of Schizosaccharomyces Pombe?

Question

[Shaojiang Cai]

Hi, all,

We have two sets of contigs assembled by Trinity and Oases (on S.pombe). We would like to compare the performance of them in terms of full length transcripts. I understand that a transcriptome depends on the condition when it was sequenced. But is there some annotated transcripts are relatively "complete"? By "complete" I mean it captures splicing forms of the genes.

I have found Pombase, which provides genome and genes but no transcripts. Also there is a Science paper from Broad Institute, which provides transcripts in FASTA format (http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiHome.html). Is this dataset good for my application? Or any other one is better?

Thanks

Answer 1

[Josh Herr]

When it comes to Schizosaccharomyces I think the best you are going to get (as far as splicing forms, etc.) is the Broad database. You can download the data here. The transcripts are listed as "transcripts.fasta" and the annotation file is the "transcripts.gtf" file.

I'm not aware of any other transcriptome database information other than what you have mentioned, so I think your only option is to sequence your own transcriptome using your strain and culture conditions.