I am working on a plant gene family. The family has ~12000 genes. I have Protein and CDS sequences in fasta format. I want to identify their gene ontologies and KEGG pathways.
I am using Blast2GO tool, but it has limitation for large number of genes.
Is there any tool or procedure (blast system for GO identification) that may be helpful for this analysis?
There are some tools available for this task depends on how and on what platform you want to work. Look and select the program and platform you want to use
ftp://ftp.geneontology.org/go/www/GO.tools.annotation.shtml
ftp://ftp.geneontology.org/go/www/GO.tools.microarray.shtml
ftp://ftp.geneontology.org/go/www/GO.tools_by_type.visualization.shtml
Hello Athar,
If you still want to use blast2Go, you can run first your blast remotely (using BLAST+ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) and save the results in an xml file, the same format as the one blast2Go produces (I think it is outfmt 5). Then you can upload the file with the results on blast2go and get your GO terms.
Alternatively, you can use Interpro http://www.ebi.ac.uk/interpro/
Hello
I usually do this: blast my query against ortholog genes (you can download them from orthoDB). I used the CoGe plataform and then you can stract the fasta protein sequences from your blast results. Then go to OrthoVenn to get the clusters and GOs
Hi Athar,
I usually used eggNog mapper, available online (http://eggnogdb.embl.de/#/app/emapper) or in github (https://github.com/jhcepas/eggnog-mapper). The output will give you COG and KEGG id. You cancellare try also tio use BlastKoala from kegg website to assign kegg id.
Best,
may be these link can help you in regard to KEGG
https://www.kegg.jp/ghostkoala/
https://www.genome.jp/kaas-bin/kaas_main
@anupam Thank you so much . Its a nice tool and can carry KEEG pathways just using fasta protein sequence. It is also fast process for large number of genes.
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