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Via Perl you will find it quite easy to build code to query for SNPs. There is a web browser GUI tool (<a href="http://www.ensembl.org/biomart/martview/ad23fb5685e6aecb59ab12ce73c89731" rel="nofollow noreferrer">HERE</a>) for building perl scripts based on which database and dataset you wish to query using Biomart library. Instructions <ol> <li>Go to <a href="http://www.ensembl.org/biomart/martview/ad23fb5685e6aecb59ab12ce73c89731" rel="nofollow noreferrer">http://www.ensembl.org/biomart/martview/ad23fb5685e6aecb59ab12ce73c89731</a> (for supported Metazoans), or <a href="http://biomart.vectorbase.org/biomart/martview/6e274bc00b3c68a131a6947d02039ade" rel="nofollow noreferrer">http://biomart.vectorbase.org/biomart/martview/6e274bc00b3c68a131a6947d02039ade</a> (for up to date Vectors of Malaria, e.g. <a href="https://www.vectorbase.org/organisms/anopheles-gambiae" rel="nofollow noreferrer">A. gambiae</a>)</li> <li>Select the database and dataset: <img src="https://i.stack.imgur.com/0SUHk.png" alt="enter image description here"></li> <li>Click on the "perl" button to generate perl code for the Biomart API querying, and copy-paste the code into your perl editor - run it with the SNP rsNumbers of your choice.</li> </ol> <blockquote> <pre><code># An example script demonstrating the use of BioMart API. use strict; use BioMart::Initializer; use BioMart::Query; use BioMart::QueryRunner; my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/." my $action='cached'; my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,'action'=>$action); my $registry = $initializer->getRegistry; my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default'); $query->setDataset("hsapiens_snp"); $query->addAttribute("refsnp_id"); $query->addAttribute("refsnp_source"); $query->addAttribute("chr_name"); $query->addAttribute("chrom_start"); $query->formatter("TSV"); my $query_runner = BioMart::QueryRunner->new(); ############################## GET RESULTS ########################## $query_runner->execute($query); $query_runner->printHeader(); $query_runner->printResults(); $query_runner->printFooter(); ##################################################################### </code></pre> </blockquote>
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1. POMap SNP IDs to genome coordinates
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