Functional annotation pipeline

Question

[sbchua.1990]

I have assembled a transcriptome using Trinity and clustering it using CD-hit with 0.95 threshold to reduce redundancy.

For the clustered transcripts, I performed blastx against nr database (restricted to basidiomycota taxon due to computational power). I imported the blast result into blast2GO to retrieve GO terms.

Using the same clustered transcripts, I used Transdecoder (default settings) to predict protein sequences. Then, the protein sequences (Transdecoder outputs) were used as queries in http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/cog/ and http://www.kegg.jp/blastkoala/ for functional annotations for both COG and KEGG.

I have seen others perform blastx on both COG and KEGG database therefore not too sure about my different approaches.

Am I heading toward right direction?

[h.mon]

Nothing wrong with your approach, but you will be left with the task of integrating the data.

I would use Trinotate to annotate a Trinity assembly. It annotates with blast and hmmer searches against uniprot and pfam, respectively, and the infers GO annotations from those. Additional blast searches may be loaded as well, but these are not used for GO anotation.

[sbchua.1990]

Thanks for your reply. I would consider your recommendation.

Answer 1

[colindaven]

I like Interproscan for functional annotation. It is surprisingly quick and easy to use, as long as you don't try to run it on a cluster.

https://github.com/ebi-pf-team/interproscan