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Old 04-09-2012, 05:46 PM   #1
fizzle123456789
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Default How to find SNP's in various genes

Hi,

Im a biochemistry student and im having trouble answeing a question which my report is based on, below is the question;

A number of single nucleotide polymorphisms (SNP) have been identified in the protein, apolipoprotein L1 (apoL1) which is just one member of a family of six conserved proteins. You will perform computer analysis to identify SNPs in apoL1 and the other five members of this protein family.

I just need to be pointedin the right direction, so far this is what i have:

http://www.ncbi.nlm.nih.gov/projects...&orien=forward

now im not quite sure how to "find" SNP's as i do not have ny sequences of my own. As represented in the link above, is this the way to identify SNP's, the mrna sequence NM_003661.3, is mapped onto the contig chromosome 22 sequence NT_011520.12.

Using CLustal W i aligned the mrna to the contig chromosome sequence but the SNP's are not on the sequence.

This is very confusing, can i actually find any other SNP or do i just use the ones on the dbSNP?

if anyone could help me in anyway i would greatly apprciate it!

Thanks


Firat
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Old 04-10-2012, 06:21 AM   #2
fizzle123456789
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can anyone help me?
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Old 04-10-2012, 12:37 PM   #3
Alex Renwick
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"perform computer analysis to identify SNPs" is vague. Ask your instructor for clarification.
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Old 04-10-2012, 12:45 PM   #4
fizzle123456789
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Quote:
Originally Posted by Alex Renwick View Post
"perform computer analysis to identify SNPs" is vague. Ask your instructor for clarification.


I did but he just said you line up the mrnas of all the apoL genes and you look for snp's.


which dodnt quite make sence to me as the question is asking for snp's in each gene rather than the differences between each of the apoL proteins.

my instructer is away till the end of this month and i need to get some work done hence here i am trying to find out what i could do in the mean time, i will see him asap but thats a while away and i need help now

what would you understand from this question?, i mean i could look for snp between a human apoL1 and a chimpanzee apoL1 by clustal W.

Im just wondering if you can identify snp's in an mrna sequence any other way but havinf mra's for lets say apol1 and comparing them to the human contig chr 22 sequence.

ahhh soo much work so little time.

thanks for you help anyway
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Old 04-10-2012, 06:42 PM   #5
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seems you need to do some more reading!
Here is the mRNA-seq analysis guide = http://seqanswers.com/wiki/How-to/RNASeq_analysis
you would need to do the alignments on the entire genome, but then can limit variant calling to just your gene of interest
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Old 04-10-2012, 06:55 PM   #6
fizzle123456789
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Quote:
Originally Posted by bioinfosm View Post
seems you need to do some more reading!
Here is the mRNA-seq analysis guide = http://seqanswers.com/wiki/How-to/RNASeq_analysis
you would need to do the alignments on the entire genome, but then can limit variant calling to just your gene of interest
So what do I exactly align? The human genome against Other organisms.

I thought to find SNP's you would have lots of mRNA from lots of different populations then map onto ref human chromosome.

Or am I wrong. To identify what a person would say is a snp, they would need more than 1 different human DNA/mRNA to create a gene 'consensus' sequence.

I'm sorry im just having trouble getting my head around it but could you explain in a little more detail.

Thanks soo much
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Old 04-12-2012, 03:53 AM   #7
fizzle123456789
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Anyone, I just need a little help?
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Old 04-12-2012, 10:24 AM   #8
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Mmm based on the info you've given I think it could be just as simple as what he said: "line up the mrnas". The link you've given shows the entry "apol1 transcript variant 1" and the next entry reads "apol1 transcript variant 4". Of course I can't get into your instructor's head but from what I understood you could just download all those transcript variants for each gene in the family and line them up using Clustal or something.


Edit: Worthy of mentioning, differences between transcript variants are not really SNPs so I'm not even sure this is what you should do. I'm just saying this based on what he told you, not what I would actually do with the initial question.

Last edited by vv85; 04-12-2012 at 12:53 PM.
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Old 03-10-2014, 11:38 PM   #9
shayeste
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hello
I want to know the exon number of SNPs such as rs12569232
please help me
thank you
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Old 03-11-2014, 05:36 AM   #10
TiborNagy
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Similar question with answer:
http://seqanswers.com/forums/showthread.php?t=41572
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