to decide whether a mutation is non-synonimous or not

zslee · 12-07-2009, 11:37 PM

i have short solexa sequences mapping to genome, in some positions there're
some certain enriched mutations, how do i know whether this mutation is non-synonimous or not ?
one method is download transcript isoforms and coding annotations from ucsc, then count from the coding start site to determine what codon this position belong to then go to codon - Aa table t ocheck, can anyone give me better method ? thanks in advance

also, i have checked, in biomart we can download phase information ~
maybe i will use this

ZSL

brasj · 12-08-2009, 06:28 AM

Is this human genomic? If it is, we have been using SIFT for this with great success.

zslee · 12-08-2009, 04:54 PM

Quote:

Originally Posted by brasj

Is this human genomic? If it is, we have been using SIFT for this with great success.

SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function
my work is simpler, i just want to know whether a change of bases on human genome affect the amino acide coded, maybe SIFT can be used next step of my project,
so thanks a lot ~~

krobison · 12-09-2009, 06:29 AM

Your original proposal is pretty much the definition of how to do it; under what metric is it less than ideal?

swbarnes2 · 12-09-2009, 09:00 AM

I would think BLASTx is the tool of choice here. You determine where in your sequence your change is, and make sure that the BLASTx match covers that letter.

krobison · 12-10-2009, 06:54 AM

No, BLASTX is very poor choice for multiple reasons:

1) Misclassifications, both false positive & false negative, around splice junctions
2) Speed. Much slower than doing lookup.
3) Very short exons will be missed
4) More risk of confusing paralogs & pseudogenes with your actual gene

Mapping the position to annotated transcript(s) and then computing the new codon & comparing its translation to the old codon is fast, simple & guaranteed. Hard to see why one would choose slow & error-prone over that.

brasj · 12-10-2009, 09:22 AM

guys, give sift a look.

you stick all your variants in there and it outputs a list of all of them that are coding and the change it does in the protein. Additionally, it also gives them a score of "tolerability".

if I understood correctly, this does all you need... and more

Assuming this is human dna, of course.

zslee · 12-10-2009, 04:56 PM

thanks to you all
i 'll first use krobison's suggestion and consider sift later
~~

colindaven · 12-11-2009, 04:55 AM

There is another thread on this topic -

http://seqanswers.com/forums/showthread.php?t=3236

Myself and some others have already developed scripts for this.
Sift is good, but is for the human genome only.

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12-07-2009, 11:37 PM	#1
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	to decide whether a mutation is non-synonimous or not i have short solexa sequences mapping to genome, in some positions there're some certain enriched mutations, how do i know whether this mutation is non-synonimous or not ? one method is download transcript isoforms and coding annotations from ucsc, then count from the coding start site to determine what codon this position belong to then go to codon - Aa table t ocheck, can anyone give me better method ? thanks in advance also, i have checked, in biomart we can download phase information ~ maybe i will use this ZSL Last edited by zslee; 12-07-2009 at 11:57 PM.

12-08-2009, 06:28 AM	#2
brasj Member Location: Washington dc Join Date: Aug 2008 Posts: 13	Is this human genomic? If it is, we have been using SIFT for this with great success.

12-09-2009, 06:29 AM	#4
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	Your original proposal is pretty much the definition of how to do it; under what metric is it less than ideal?

12-09-2009, 09:00 AM	#5
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	I would think BLASTx is the tool of choice here. You determine where in your sequence your change is, and make sure that the BLASTx match covers that letter.

12-10-2009, 06:54 AM	#6
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	No, BLASTX is very poor choice for multiple reasons: 1) Misclassifications, both false positive & false negative, around splice junctions 2) Speed. Much slower than doing lookup. 3) Very short exons will be missed 4) More risk of confusing paralogs & pseudogenes with your actual gene Mapping the position to annotated transcript(s) and then computing the new codon & comparing its translation to the old codon is fast, simple & guaranteed. Hard to see why one would choose slow & error-prone over that.

12-10-2009, 09:22 AM	#7
brasj Member Location: Washington dc Join Date: Aug 2008 Posts: 13	guys, give sift a look. you stick all your variants in there and it outputs a list of all of them that are coding and the change it does in the protein. Additionally, it also gives them a score of "tolerability". if I understood correctly, this does all you need... and more Assuming this is human dna, of course.

12-10-2009, 04:56 PM	#8
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	thanks to you all i 'll first use krobison's suggestion and consider sift later ~~

12-11-2009, 04:55 AM	#9
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	There is another thread on this topic - http://seqanswers.com/forums/showthread.php?t=3236 Myself and some others have already developed scripts for this. Sift is good, but is for the human genome only.