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Old 07-06-2009, 06:48 PM   #1
anyone1985
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Default MUMmer VS blastp

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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Old 07-06-2009, 11:25 PM   #2
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yes, you can try BSR, it is based on blastp.
http://www.microbialgenomics.org/BSR/
good luck!
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Old 07-07-2009, 12:13 AM   #3
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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.
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Old 07-07-2009, 07:43 PM   #4
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Quote:
Originally Posted by anyone1985 View Post
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.
"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.
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Old 07-08-2009, 04:20 AM   #5
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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.

Quote:
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 Images
File Type: jpg ortholog plots.jpg (18.8 KB, 47 views)
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Old 06-24-2010, 12:05 PM   #6
rahul.m.dhodapkar
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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=536870908
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Old 06-24-2010, 03:30 PM   #7
robs
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Try:
http://seqanswers.com/wiki/Talk:MUMmer

The corresponding paper can be found here:
http://bioinformatics.oxfordjournals...ull/25/13/1609
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Old 06-24-2010, 05:50 PM   #8
rahul.m.dhodapkar
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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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Old 06-24-2010, 05:58 PM   #9
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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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Old 06-24-2010, 06:02 PM   #10
rahul.m.dhodapkar
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@robs

thanks so much for your help.
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Old 11-30-2010, 03:26 PM   #11
Will Nelson
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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).
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Old 12-08-2010, 01:41 AM   #12
flxlex
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Quote:
Originally Posted by Will Nelson View Post
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).
First, thanks for, as far as I can tell, the only solution to the mummer textlen problem on the web...

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
to the src/kurtz/libbasedir/types.h file before the line where it says

Code:
#ifdef SIXTYFOURBITS
and then run

Code:
make install
again.

(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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Old 04-20-2012, 02:08 AM   #13
colindaven
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This thread also supplies another solution:

http://sourceforge.net/projects/mumm.../topic/2072496

"
If you recompile the package like so:

> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"

you should have no more problems with space limitations.

Best,
-Adam
"
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Old 02-11-2013, 08:52 AM   #14
cindy0805
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I want to compare to genomes with 87%similarity, I cant decide should I use Promer or NUCMER?
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