I just finish a bacteria genome, then compare two genomes of the same genus. I hesitate between the MUMmer and blastp. Please give me some suggestions. And also, is there any software to get a dot plot from the result of blastp?
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yes, you can try BSR, it is based on blastp.
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good luck!
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Originally posted by anyone1985 View PostI think accurately I'd like to get a dot plot of two genomes's ortholog plot by reciprocal best-hit pair from the result of pair-wise BLASTP.
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Yes, promer is pretty good. However, I'd like to draw the graph exactly. The promer can not give a clear position to identify the gene. Many literatures have figures as below. I am intrested in which software can draw such figure.
Originally posted by Torst View Post"promer" from the Mummer suite will effectively do want you want. Although it doesn't examine "genes" it matches translated regions, which if there is a good match, are likely to be orthologs (or paralogs) anyway.Attached Files
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Try:
The corresponding paper can be found here:
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@robs
thanks, but the link says:
[Thanks for the hint about the recent "MEMs" implementation that "can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3". Seems to be working perfectly where MUMmer crashed :-) --Dan 15:08, 5 January 2010 (UTC)]
what was the original hint? (sorry for any stupidity)
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Not sure what you mean with "original hint". There is only one hint and if you take a look at the paper you will see that the quote is actually from there.
The MEMs implementation has a mummer module that can be used instead of the MUMmer3 one. By doing this, mummer shouldn't crash anymore. More details are in the paper.
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Originally posted by Will Nelson View PostTo solve the textlen problem, build a 64-bit version, and make sure
#define SIXTYFOURBITS is set in types.h.
(Grep for the one place this is used, to see where to set it).
Not being an hardcore programmer, but a biologist-come-bioinformatician (more like a user of programs), it took me some time to figure out how to implement it, though. What you meant was to add this line
Code:#define SIXTYFOURBITS
Code:#ifdef SIXTYFOURBITS
Code:make install
(I had begun to 'uncomment' the ifdef line, causing all kinds of errors - like I said, not a programmer)
Just clarifying for future generations...
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