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Old 12-20-2010, 05:40 AM   #1
Stephanbio
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Location: Netherlands

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Default Convert chromosomal position to gene sequence position

I have a list of mutations with their chromosomal locations like
chr1:6266188-6266188
chr22:5443534-5443534 .....

I know how to fetch a list of genes with ucsc browser and/or galaxy that intersects with my mutations. and their accompanying DNA sequence

But in order to know wich nucleotide in the gene sequence is mutated I have to know the position in the gene.
Is there a way to convert the chromosomal position to nucleotide position in a gene. so that I can easy invistigate what kind of mutation it is.
dream result would be:
gene1 blabla lenght: 1...789 your mutation is in place 88
or actaXacta
or actaNacta
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Old 12-20-2010, 11:40 AM   #2
ZhengXia
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Default

If you fetch gene region from annotation database such as UCSC knowngene.txt, you can easily do it.
Quote:
Originally Posted by Stephanbio View Post
I have a list of mutations with their chromosomal locations like
chr1:6266188-6266188
chr22:5443534-5443534 .....

I know how to fetch a list of genes with ucsc browser and/or galaxy that intersects with my mutations. and their accompanying DNA sequence

But in order to know wich nucleotide in the gene sequence is mutated I have to know the position in the gene.
Is there a way to convert the chromosomal position to nucleotide position in a gene. so that I can easy invistigate what kind of mutation it is.
dream result would be:
gene1 blabla lenght: 1...789 your mutation is in place 88
or actaXacta
or actaNacta
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Old 12-20-2010, 11:43 PM   #3
Stephanbio
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Default

Now that's exactly my question! If it's so easy, can you explain further

Last edited by Stephanbio; 12-21-2010 at 12:05 AM.
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Old 12-21-2010, 01:09 AM   #4
Jonathan
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http://seqanswers.com/wiki/ANNOVAR

is what your are looking for.
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Old 12-21-2010, 07:10 AM   #5
Joann
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Default more open research

I suggest ANNOVAR for publication in the new journal Open Research Computation--recently introduced elsewhere on this site.
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Old 12-21-2010, 07:12 AM   #6
Stephanbio
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Default

Thanx , I think ANNOVAR is exactly what i need
I'm playing with it right now.
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