MUMmer VS blastp

anyone1985 · 07-06-2009, 06:48 PM

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?

bio-x · 07-06-2009, 11:25 PM

yes, you can try BSR, it is based on blastp.
http://www.microbialgenomics.org/BSR/
good luck!

anyone1985 · 07-07-2009, 12:13 AM

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.

Torst · 07-07-2009, 07:43 PM

Quote:

Originally Posted by anyone1985

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.

anyone1985 · 07-08-2009, 04:20 AM

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

"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.

rahul.m.dhodapkar · 06-24-2010, 12:05 PM

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

robs · 06-24-2010, 03:30 PM

Try:
http://seqanswers.com/wiki/Talk:MUMmer

The corresponding paper can be found here:
http://bioinformatics.oxfordjournals...ull/25/13/1609

rahul.m.dhodapkar · 06-24-2010, 05:50 PM

@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)

robs · 06-24-2010, 05:58 PM

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.

rahul.m.dhodapkar · 06-24-2010, 06:02 PM

@robs

thanks so much for your help.

Will Nelson · 11-30-2010, 03:26 PM

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).

flxlex · 12-08-2010, 01:41 AM

Quote:

Originally Posted by Will Nelson

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...

colindaven · 04-20-2012, 02:08 AM

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
"

cindy0805 · 02-11-2013, 08:52 AM

I want to compare to genomes with 87%similarity, I cant decide should I use Promer or NUCMER?

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07-06-2009, 06:48 PM	#1
anyone1985 Member Location: shanghai, chia Join Date: Mar 2009 Posts: 67	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?

07-06-2009, 11:25 PM	#2
bio-x Member Location: China Join Date: Nov 2008 Posts: 18	yes, you can try BSR, it is based on blastp. http://www.microbialgenomics.org/BSR/ good luck!

07-07-2009, 12:13 AM	#3
anyone1985 Member Location: shanghai, chia Join Date: Mar 2009 Posts: 67	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.

06-24-2010, 12:05 PM	#6
rahul.m.dhodapkar Member Location: New Haven Join Date: Jun 2010 Posts: 28	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

06-24-2010, 03:30 PM	#7
robs Senior Member Location: San Diego, CA Join Date: May 2010 Posts: 116	Try: http://seqanswers.com/wiki/Talk:MUMmer The corresponding paper can be found here: http://bioinformatics.oxfordjournals...ull/25/13/1609

06-24-2010, 05:50 PM	#8
rahul.m.dhodapkar Member Location: New Haven Join Date: Jun 2010 Posts: 28	@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)

06-24-2010, 05:58 PM	#9
robs Senior Member Location: San Diego, CA Join Date: May 2010 Posts: 116	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.

06-24-2010, 06:02 PM	#10
rahul.m.dhodapkar Member Location: New Haven Join Date: Jun 2010 Posts: 28	@robs thanks so much for your help.

11-30-2010, 03:26 PM	#11
Will Nelson Member Location: Arizona Join Date: Nov 2010 Posts: 16	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).

04-20-2012, 02:08 AM	#13
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	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 "

02-11-2013, 08:52 AM	#14
cindy0805 Junior Member Location: Netherland Join Date: Jan 2013 Posts: 1	I want to compare to genomes with 87%similarity, I cant decide should I use Promer or NUCMER?