Question: Functional annotation pipeline
0
gravatar for sbchua.1990
4 months ago by
sbchua.199010
sbchua.199010 wrote:

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?

blast rna-seq sequence assembly • 293 views
ADD COMMENTlink modified 9 weeks ago by colindaven280 • written 4 months ago by sbchua.199010
2

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by h.mon8.6k

Thanks for your reply. I would consider your recommendation.

ADD REPLYlink written 3 months ago by sbchua.199010
0
gravatar for colindaven
9 weeks ago by
colindaven280
colindaven280 wrote:

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

ADD COMMENTlink written 9 weeks ago by colindaven280
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