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Presently I am working on metagenomics of coal biomethenation by bacterial consortium.

I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence. I have gone through different database like Metacyc, Biocyc etc. Please help me that how can I draw an inference towards the metabolic enzyme that are involved in biomethenation of coal.

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2 Answers 2

Well first off, we don't know how you sequenced the data. What did you actually sequence? Did you look at transcriptional activity using RNA-seq or did you do a full genome sequencing. Were there any paired-end reads? How did you create your library? Did you enrich the bacterial consortium for biomethanation activity?

Where do you reads map? The consortium complicates things but you will likely need to build a quality contig library before you do anything else. Without a doubt, much of your library will not map to anything interesting but you should still annotate the library by seeing where the reads map up. Identifying ORFs will be useful.

Likely, you will have a set of genes that will be involved with biomethanation. You should BLAST the bejesus out of your contig library for hits. Do they match any of your ORFs? Going the otherway, do your ORFs match any of the genes in EcoCyc or BioCyc. Do you need to use a larger database?

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The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you unclear on ligands in many cases. So, the final step is to clarify the function with biochemical lab methods.

So, if you are stuck with a huge sequence, first try to find the genes in it.

http://en.wikipedia.org/wiki/Gene_prediction

For subsequent annotation/classification, I recommend InterPro and PROSITE.

http://www.ebi.ac.uk/Tools/pfa/iprscan/

http://prosite.expasy.org/scanprosite/

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