Semi-Automatic Protein Annotation (like BLAST2Go)

Question

[sdbaney]

I have paired-end RNA-Seq reads that were assembled via Trinity de novo assembly. These transcripts were then run through Cuffdiff to generate gtf files of differentially expressed 'genes'. We do not have a reference genome (non-model organism). I have sorted the files to keep the significant data but now want to run this through an annotation program in order to get more information about what these proteins may be. I still have about 10,000 lines in this gtf file so manually blasting is not an option. My advisor recommended BLAST2go but I was wondering is this is an outdated tool? Are there are any better ones out there?

Answer 1

[h.mon]

As far as I know, Blast2GO is not outdated, on the contrary, it is constantly updated, and their site also says so:

Latest Versions

Highlights of Version 5.2 (Aug 2018)

However, I don't use it, and I can't vouch for its quality. If you have a Trinity assembly, you could try Trinotate, which is developed by the same group which developed Trinity, and is tightly integrated with it.