I am working with Next Generation Sequencing. I BLASTed the bovine de novo assembled contigs to the NCBI nucleotide database. I got a matching with a lot of species i.e. different kind of bacteria, viruses and mammals. I want them to group in a logical way i.e. all the bacteria in one group (bacteria group) similarly viruses and mammals. This is hard to arrange manually, can anybody help how I can arrange my vast number of species into some logical grouping. Thanking in anticipation.
This is basically metagenomics. Congratulations, you already did the most time consuming step. There are several ways to go from there, but I will talk about the one I know best. There is the metagenomic analysis tool MEGAN. It can read your Blast Output, if it is in the correct format (normal XML or tabular) and will automatically do what you want. For a start, just use the default values, for more help you an then go to the Community Website of MEGAN for help.
Analysing your data may take a little, depending on how many contigs you have. But if you were able to blast them in reasonable time it should be no problem. As I said, you are through the most time consuming step already.