Question: Functional annotation pipeline
gravatar for sbchua.1990
23 months ago by
sbchua.199030 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 and 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 • 1.3k views
ADD COMMENTlink modified 21 months ago by colindaven1.2k • written 23 months ago by sbchua.199030

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 23 months ago • written 23 months ago by h.mon24k

Thanks for your reply. I would consider your recommendation.

ADD REPLYlink written 23 months ago by sbchua.199030
gravatar for colindaven
21 months ago by
Hannover Medical School
colindaven1.2k 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.

ADD COMMENTlink written 21 months ago by colindaven1.2k
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