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I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be preferable.

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  • $\begingroup$ I have made some major edits to to your question to stop it being closed for HWK. Feel free to roll back :) $\endgroup$ – James Jan 12 '15 at 15:26
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You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll give you an answer to get you started on your research.

Example

An excellent example of such a study is Fellay et al., 2007 and you can find their materials and methods supplement here.

An introduction to this kind of research

First you need to find the sequences of proteins that you think are significant. There are a bunch of ways of doing this, but I suggest standing on the shoulders of giants and scouring the literature (regardless, find an example where this has been done elsewhere). If there isn't much out there or for an entirely new viewpoint on something, this answer might help for finding proteins in the DNA sequence.

Sequence alignments against other strains is your best bet of identifying mutations (and possibly an indicator of resistance, which is what I guess you're after). There are plenty to choose from, but BLAST is a good tool to start with. You should compare your resistant strain with non resistant strains. Be very careful when analysing the data, not every mutation will be significant.

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  • $\begingroup$ Thanks for trying to help me. Nice photos you take, you are a talented photographer. I have 1000 books on bioinformatics and years of software engineering and computations experience. I need a rational way and the best software for mutation analysis. I don`t like microbes at all. $\endgroup$ – VassiaAlk Jan 12 '15 at 19:49
  • $\begingroup$ biostars.org are a community with a focus on the software/programatic side of biology. Perhaps you could reframe your question there? $\endgroup$ – James Jan 14 '15 at 23:30

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