Processing Blast output for Blast2GO

[JueFish]

Hello all,

I've been trying to figure out how the taxonomy ids are set up for NCBI Blast results, but have been having some trouble. I am trying to figure out how to include/exclude results from Blast searches based on the associated taxa that Blast results associated with each sequence blasted. In other words, I want to be able to pull out all the sequences that blast to E. coli or Stronglyocentros purpuratus or, more generally, Eukaryotes, whatever, and then be able to import them into a program like Blast2GO to run some stats on them. I thought perhaps I could pull out a series of sequence names to use for filtering using some unix or python commands, but I haven't been able to figure out how to use the taxonomy ids to do that. Has anyone done this before with a decent sized data set (a few thousand sequences) and have some good suggestions?

Thanks in advance any advice.

[flxlex]

You could use MEGAN, http://www-ab.informatik.uni-tuebing...oftware/megan/. It allows for selecting a part of the taxonomic tree, and fetching all the reads that have a hit to that part (select a node, 'select subtree' from the menu, export the reads through the menu). Drawback is that it needs the blast output file as input, but you can restrict the output to just the first x alignments and no description lines to keep the file smaller.

[JueFish]

I'll check it out. Thanks for the suggestion. I was able to come up with long way around this issue, but would much rather find a way to figure out the taxonomy codes so I could either code a solution or find one already out there. Does anyone know of where I could find a good description of how the hierarchy of the NCBI taxon ids is set-up? I looked around the website and couldn't find much that was useful.

[Chuckytah]

You could use MEGAN, http://www-ab.informatik.uni-tuebing...oftware/megan/. It allows for selecting a part of the taxonomic tree, and fetching all the reads that have a hit to that part (select a node, 'select subtree' from the menu, export the reads through the menu). Drawback is that it needs the blast output file as input, but you can restrict the output to just the first x alignments and no description lines to keep the file smaller.

Mine gives me an error