Annotating a novel transcriptome

[michael-steffen]

I am trying to annotate a novel transcriptome, which will then be used to compare expression levels between individuals and tissues. I have CLC genomic workbench and what I was doing is blasting subsets of my assembled illumine transcriptome to figure out what I have. However, there seems to be some trouble with this. 1) its super slow 2) When blasting chunks, it almost always partially fails and does not give back hits(or saying it can't find any) for a number of sequences. Even when I re-blast these pieces, I get different numbers of blast hits back.

I'm not sure if this crappy blasting is the result of NCBI or CLC, but either way, its not really acceptable if I am not getting back results. I could individually blast each of the contigs to ncbi to figure out what they are, but considering i got over 24,000 sequences to blast, I was hoping their would be a better way.

Also, is there I way to remove singletons from my assembled contigs? I am guessing I don't want to annotate these guys.

Assuming this had all worked, I could have used blast2go and set up everything that I wanted I think...

So, what would be the best way to annotate my novel genome? I have been trying to figure this out, but its being very difficult for me and causing me a lot of frustration. I got no one in my department who can help.

Thanks,
Mike

[FastAnnot]

Have you resolved this problem? If not then you might consider our annotation service www.fastannot.com. It is not free, but it is not too expensive either. Annotating against nr is a big task. If you did solve your problem already, would you care to share how you did it?