Secondary Metabolite

[Aeolus Huios]

Dear all,

I got genome sequence From NCBI in gbk format and i converted into FASTA format. I would Like to know how to extract only the sequences which involve only in secondary metabolite function from the genome fasta sequence. Can anybody help me out to solve this problem.

I will happy and grateful to get help.

With regards,
Aeolus

[arvid]

Are you experienced in writing scripts (e.g. Perl or Python) and working with a well-annotated organism? Then you could use the Bio APIs and parse the original GenBank file(s), matching the sequence records against certain functional annotation, such as the enzyme class (EC_number in GenBank) that you gathered from e.g. KEGG to belong to the kind of secondary metabolism pathways you are interested in.
For some BioPython examples have a look at this link:

http://wilke.openwetware.org/Parsing_Genbank_files_with_Biopython.html

[Aeolus Huios]

Hi Arvid,
Thanks for reply!
Yes I am working in Cyanobacteria genome strain 51142 which have well annotated sequences. I would like to separate the sequences which are involve in Secondary metabolism. So, I am little bit can handle bioperl modules. So ac You suggest some more help. It will be more well appreciated! :-)

With regards,
Aeolus

[arvid]

I'm not a BioPerl user (I'm using BioPython), but I'm sure others can chime in on details if you post some code or specific problem (what you're asking for is still very general). Did you search for existing scripts for similar parsing already? I'm sure there are BioPerl tutorials for parsing GenBank files and selecting records and features based on annotation, like the link I posted for BioPython parsing.

EDIT: This HOWTO would be a place to start: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Beware that everything depends on your definition of "Secondary metabolism", which you have to define very clearly to get useful results - e.g. one way would be to look up the appropriate KEGG pathways (you can parse the KEGG flat files with the Bio APIs as well) and make a list of "Secondary metabolism"-related enzyme codes. Then, parse the GenBank file and filter for enzymes codes contained in your list.