Mapping reads against metabolical maps

A_Morozov · 08-14-2013, 11:56 PM

I need to make a functional analysis of a metagenome and therefore have to map a lot of color space SOLiD reads 75 bp each (sadly, assembly isn't any good) against metabolical pathways. Desired output will be something like a KEGG map, with every protein marked "Found in metagenome, reads #XXXXXXX, #YYYYYY" or "Not found".
The first idea was a KEGG Mapper set of programs, but it requires KEGG orthologies as input, and getting those for every read without an account will require some creative hacking and violate their license. Are there any other big DBs for pathway maps, ideally linked to PFAM/Genbank/whatever for easy understanding?

A_Morozov · 08-16-2013, 01:15 AM

I think I found what I was looking for, posting here in case someone will find it useful. Brenda Enzymes DB allows to get lots of enzyme information via SOAP interface, including accession codes for organisms. And further mapping will be straightforward.

FTillett72 · 11-16-2016, 03:07 PM

That's good. Thanks because I had the same problem

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08-14-2013, 11:56 PM	#1
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	Mapping reads against metabolical maps I need to make a functional analysis of a metagenome and therefore have to map a lot of color space SOLiD reads 75 bp each (sadly, assembly isn't any good) against metabolical pathways. Desired output will be something like a KEGG map, with every protein marked "Found in metagenome, reads #XXXXXXX, #YYYYYY" or "Not found". The first idea was a KEGG Mapper set of programs, but it requires KEGG orthologies as input, and getting those for every read without an account will require some creative hacking and violate their license. Are there any other big DBs for pathway maps, ideally linked to PFAM/Genbank/whatever for easy understanding?

08-16-2013, 01:15 AM	#2
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	I think I found what I was looking for, posting here in case someone will find it useful. Brenda Enzymes DB allows to get lots of enzyme information via SOAP interface, including accession codes for organisms. And further mapping will be straightforward.

11-16-2016, 03:07 PM	#3
FTillett72 Junior Member Location: Poland Join Date: Nov 2016 Posts: 1	That's good. Thanks because I had the same problem