How To Blast Kegg-Only Data In The 'Nr' Database

Question

[Shuixia100]

Hi there,

I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.

Here is my approach:

1. download the KO number of a specific pathway that I'm interested in from the KEGG server
2. convert the KO number downloaded into GI number
3. then use the blast+ 's gilist function to Blast the GI numbers that I downloaded.

But MY PROBLEM is: I dont know how to do the step 1 and step 2, could anyone provide some procedure to do that? Many thanks,

Kylie

[Michael]

I think that this question is not sufficiently answered, bumping. Maybe there is a way of doing this by means of blastdbcmd and extracting identifiers? While it might be useful to be able to restrict the search to a certain pathway, it might be useful to be able to extract the complete KEGG portion of NR.

Answer 1

[Rm]

Look at similar posts:

http://www.biostars.org/post/show/3133/is-there-any-way-to-retrieve-genes-sequences-in-fasta-format-using-the-kegg-orthology-code/#3182

http://www.biostars.org/post/show/9978/get-all-the-genes-in-a-pathway-eg-kegg/#9981

http://www.biostars.org/post/show/11789/from-gene-to-genome-from-kegg-to-ncbi/

[Michael]

I think that the references are helpful, however they do not serve as a complete answer but only go half the way. The posts all work for individual ids, but none of them shows a complete example of how to get all GIs which are derived from kegg or have an assigned EC number.

Answer 2

[jackuser1979]

I have not tried myself, but there is a bioconductor package called KEGGREST

http://bioconductor.org/packages/release/bioc/html/KEGGREST.html

Here you will find how to retrieve genes from specific pathway

http://grokbase.com/t/r/bioconductor/131xffyqg7/bioc-kegg-rest-retrieving-genes