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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?
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?
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