I have a RNA-Seq data in which I have to construct the KEGG Pathway for DGE between two samples. I also have nucleotide sequences (contigs) in the fasta format (.fa) file. Kindly tell me how to assign the KO IDs to these nucleotide sequences. Also help me in construction of pathways either using KEGG, Cytoscape or any other pathway network builder software/server.
hi Punith,
you might also want to check out Trinotate. (http://trinotate.github.io/)
they describe step by step how to annotate assembled RNA sequences, including Kegg.
Hope this helps.
Fritz
Dear Punith
The best way is to use Galant plugin in Cytoscape which solves the purpose that you aim for. Please make sure that the ids are obtained from nuc sequences using NCBI's batch entrez before you construct the pathway networks.
Hope this helps
Prash
hi Punith,
you might also want to check out Trinotate. (http://trinotate.github.io/)
they describe step by step how to annotate assembled RNA sequences, including Kegg.
Hope this helps.
Fritz
Dear Punith,
You can consider using Blast2GO (https://www.blast2go.com/) to annotate your sequences. This tool will annotate them with KEGG ID but also using GO and InterPro terms.
Best,
Juan
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