How To Get The Effect Of A Snp On A Transcript Via Eutils
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13.9 years ago
Andrea_Bio ★ 2.8k

Esteemed bioinformaticians

I was wondering if anyone on here has a local copy of dbSNP and could answer me some questions before i undergo what i have been told is a painful process of installing a local copy.

I have looked at all of these Entrez SNP reports and none of them give me the information I want. I want to get the information about how the SNP affects the transcript as show in the GeneView section of the webpage. Some reports do show you some of this information - this is a snippet of the flat file report from rsrs2034920

LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=coding-synonymous | allele=C | frame=3 | residue=N | aaposition=97<BR> LOC | CT45A5 | locusid=441521 | fxn-class=reference | allele=T | frame=3 | residue=N | aaposition=97<BR>

You can't link the consequence info in this report to any particular transcript. There is no transcript information other than this in the whole report.

So i was wondering,

1) Am i missing something obvious and i get the information i want from these reports 2) Presumbably a local copy of dbSNP will contain all of the information used on the webpages so i can get the information from here as a last resort

Please note, I don't want to use any other SNP effect prediction tools like ensembl or snp nexus to get snp consequence - it has to be dbSNP.

my humble thanks

dbsnp eutils snp • 3.3k views
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4
Entering edit mode
13.9 years ago

The information you want is available in the XML report.

<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="3" protAcc="NP_001007552" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="3" protAcc="NP_001007552" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="2" protAcc="NP_001007552" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001007551" mrnaVer="2" protAcc="NP_001007552" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001172288" mrnaVer="1" protAcc="NP_001165759" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="C" residue="N" aaPosition="96"/>
<FxnSet geneId="441521" symbol="CT45A5" mrnaAcc="NM_001172288" mrnaVer="1" protAcc="NP_001165759" protVer="1" fxnClass="reference" readingFrame="3" allele="T" residue="N" aaPosition="96"/>
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what is the rettype of that report as none of the reports in the list i looked at look like that. Is it native? I think that's the default. I know you're a java programmer but I don't know if you use perl. What would you recommend for parsing xml in perl? thanks a lot

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that report wasn't in the list of reports at ncbi! However the rettype=native report doesn't give the snp allele information. There is some info for the individual submitters but i don't want to use that. I want to use the allele mapped to a specific assembly and if your snp is intronic or the like (e.g. only has one consequence for all the different alleles) you can't get the snp allele from this report

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Entering edit mode
13.9 years ago

I am not sure whether I understood your question correctly, but did you try with Biomart?

Go to biomart, select Ensembl, then DATABASE>Ensembl Variation and DATASET>dbSNP, then in the Attributes section you can get information like 'phenotype description' under 'Sequence variation' and 'Transcript ID' under 'Gene Associated Information'.

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i've never used biomart - will have a look

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giovanni i was wondering if you were still looking at this question as i have some things i would like to ask

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don't worry, ask them and open a new question if you feel it is necessary... I am not a biomart expert but I will try to answer.

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