what program do you prefer

[lisa.brown]

I've completed several RNA runs on our 454 Jr. Now I'm trying to get functional info for the reads I have that actually aren't 16 or 23S rRNA. Here is what I've done so far: 1 assembled the reads in DNASTAR to a template of 16S and 23S reads. This gave me an output file of unassembled reads. 2. I took the unassembled reads and ran the entire file (600 reads) through BLAST, limiting the output to 10 hits. 3. I've looked at each reads BLAST result to get an idea of function.

THIS APPROACH IS AWFUL!!!!

How do I gain functional data for my mRNA reads? Is there a program out there that will do this for me?!

When I assemble my raw reads from the 454 to a template for this microbe, it doesn't give me good results or anything that tells me mRNA function. I just get really deep coverage of the 16 and 23S regions.

Any help is appreciated!

[dpryan]

It sounds like you're looking for something like blast2GO.

[lisa.brown]

Thanks. I'll give it a shot. I also tried MG-RAST which gives great functional data but the problem with MG-RAST is that it doesn't provide only one annotation of each submitted read. You get many annotations for each read which is the opposite of helpful for me.