Question: Search COGs from the EggNOG collection
gravatar for Penny Liu
3.8 years ago by
Penny Liu30
Penny Liu30 wrote:

I want to classified predicted genes using the COGs (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases.

The function annotation of COGs like the publication posted below. enter image description here

For performance reasons, the online sequence mapper of EggNOG v4.5 is currently limitted to one protein sequence at a time. Multi sequence FASTA files are not allowed.

Therefore, I performed local HMMER searches.

Download all HMM models and build a HMMER database using hmmpress. Finally, use hmmscan to query protein sequences against the database.

The following is my full code:

cat bactNOG_hmm/*.hmm > bactDB.hmmer
hmmpress bactDB.hmmer
hmmscan bactDB.hmmer MyQueryFasta.fa

However, I did not get any function annotation of COGs from the output file format. Can anyone please help me out.

ADD COMMENTlink modified 3.8 years ago by Lars Juhl Jensen11k • written 3.8 years ago by Penny Liu30
gravatar for Lars Juhl Jensen
3.8 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

The easiest solution would be to use the new eggNOG-mapper, which allows you to upload a multi-fasta file:

ADD COMMENTlink written 3.8 years ago by Lars Juhl Jensen11k
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