Find The Base And Amino Acids Of The List Position Of Dna Sequence With Perl

Hi everyone,

I have two data :

SNP data:

pos_ start 14185,21066,26659....

pos_end 14185,,21066,26659....

genotype T

reference C

gen list data:

......

CDS from (5 sile): 1,1920,2205.....

CDS to (3 sile):1527,1777,2077.....

initiation codon : GTG,TTG,TTG Termination codon: CGA,CTG,CAT....

I want to know at the position of SNPs which were contained in gen list? where the position in the gene was mutated and the protein. How can I find that? I would appreciate if you could give some pointers.

perl snp bioperl

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updated 15.0 years ago by Sean Davis

• written 15.0 years ago by User 4391 •

Don't you have the absolute genomic coordinates of your SNPs?

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written 15.0 years ago by Bert Overduin

I try to understand your question, but I find myself unable to do so. Could you please improve the formatting of your example files? It is not at all clear to me what your starting point is.

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written 15.0 years ago by Lars Juhl Jensen

@Berl Overduin: I just only have a excel data. @Lars Juhl Jensen: could you show me how to insert the picture in the question? I want to insert the excel data.

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written 15.0 years ago by User 4391 •

1 answer

I would suggest that you convert your data into a format that can be used by snpEff, the Ensembl Variant Effect Predictor, or annovar and use one of those softwares to annotate your variants. Perl might be a good choice of language to do the conversion.

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written 15.0 years ago by Sean Davis

I don't know about the other tools you mention, but the Ensembl VEP needs the genomic coordinates of the variant as input. As far as I understand from the very limited information that the user provides (s)he doesn't have those .... :( Plus I don't know which genome (s)he is working with .... maybe one we don't have in Ensembl .....

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written 15.0 years ago by Bert Overduin