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I feel like this should be simple!! Help!

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I feel like this should be simple!! Help!

Postby smc8339 » Wed Jul 17, 2013 6:38 pm

Hi,

So my PI has given me the task of comparing all the genes in two different strains of Streptococcus pneumoniae (Taiwan 19F and TIGR4)
For example, he has created a similar list for TIGR4 and D39 matching all the homologous genes (SP_0001 is homologous to SPD_0045, for example).

When he showed me this, he is actually looking up each gene, taking the sequence and blasting it against the other genome. I feel like this method will take me eons and so was wondering how I blast all the genes from TIGR4 against the genome of Taiwan 19F.

I planned on downloading the FASTA files for all the genes for TIGR4, creating one file, and then uploading this and blasting it as a whole. With this I was wondering how I can best download all the gene sequences for this strain. Is this on the FTP site? Would all the genes be in the .ffn download? If so, I was able to blast this entire file against the genome, however, the way we want to identify/match genes is with the locus tag identifier and this is not one of the identifiers in this download (the .ffn).

Any advice on how best to do this would be greatly appreciated!!!!!!

Thank you in advance!
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Postby jeffz » Thu Jul 18, 2013 2:20 am

Well this method should work actually. Did you try to ask our senior for this. I think that they may help you much better then any other way. Do not get worry about the project, it would be fine.
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Postby smc8339 » Fri Jul 19, 2013 8:21 pm

Which method should work? I was shown the gene-by-gene way by my senior. I'm trying to find a faster, more efficient way of doing this. I have over 2,000 genes to look at.
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