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.
good luck! -
Thank you for bio-x's kind help. I 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. I guess there must be some software which is suitable to do this. Please give me some suggestions.Comment
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"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.Originally posted by anyone1985 View PostComment
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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 PostComment
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does anyone know how to fix the following MUMmer error?
where textlen is the same as the length of build36 (hg18)
./mummer: suffix tree construction failed: textlen=3080436075 larger than maximal textlen=536870908Comment
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Try:
http://seqanswers.com/wiki/Talk:MUMmer
The corresponding paper can be found here:
http://bioinformatics.oxfordjournals...ull/25/13/1609Comment
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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)Comment
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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.Comment
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@robs
thanks so much for your help.Comment
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To 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).Comment
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First, thanks for, as far as I can tell, the only solution to the mummer textlen problem on the web...Originally posted by Will Nelson View Post
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
to the src/kurtz/libbasedir/types.h file before the line where it saysCode:#define SIXTYFOURBITS
and then runCode:#ifdef SIXTYFOURBITS
again.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...Comment
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This thread also supplies another solution:
"
If you recompile the package like so:
> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"
you should have no more problems with space limitations.
Best,
-Adam
"Comment
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I want to compare to genomes with 87%similarity, I cant decide should I use Promer or NUCMER?Comment
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