<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Matthias<div>If you wish to use Biomart you will need to perform two queries where you get the coordinates of your snps that you want to use as start and end regions and then put these start and end positions into a second query using the base pair start and end filter. It may be easier to use the API from variation and core to get this information. Please let us know if you require help with the API.</div><div>Regards</div><div>Rhoda</div><div><br></div><div><br><div><div>On 15 Mar 2011, at 09:11, Matthias Macé wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div text="#000000" bgcolor="#ffffff">Dear all,<br>First thank you for any suggestion.<br>We are trying to get genes overlapping with segments comprised between two SNPs.<br>Input = rsID from start snp, rsID for end snp (as shown below).<br>Expected output : gene IDs<br><br>Example:<br><pre wrap="">query: rs_ID_1---------------------------rs_ID_2
<-----------gene_1------------->
<-------gene_2--------->
<-----------gene_3------------->
It would return : gene_1, gene_2, gene_3
</pre><br>We would like to perform this in a unique query (e.g. not with a first query SNP >> coordinates followed by a second coordinates >>> genes).<br><br>We tried this using Biomart (db=Homo sapiens Variation (dbSNP 132;ENSEMBL); Filters: REGION/Marker-end-start; Attributes: any ID) without success (it returns a null output). In a general way, nothing happens when using this filter.<br><br>So here comes our questions:<br>- how to use this filter ?<br>- do you have any suggestion for doing this ?<br><br><br>Best regards,<br>MM<br><br><br><div class="moz-signature">--<span class="Apple-converted-space"> </span><br><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; ">"Only two things are infinite, the universe and human stupidity, and I'm not sure about the former." -Albert Einstein</span></font></address><span class="ds16" style="font-size: 14px; font-family: 'Century Gothic'; font-weight: bold; ">Dr Matthias Macé</span><span class="ds17" style="font-size: 14px; font-family: 'Century Gothic'; ">, DVM, PhD</span><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; "><strong>INSERM U1043</strong></span></font></address><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; ">C.H.U. Purpan - BP 3028</span></font></address><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; ">31024 TOULOUSE CEDEX 3</span></font></address><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; ">tel: (33) 562 74 45 09</span></font></address><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; ">mobile: (33) 608 881481</span></font></address><address><font face="Courier New, Courier, Monaco, monospace" size="1"><span class="ds19" style="color: rgb(0, 102, 255); font-family: 'Century Gothic'; "><a href="http://www.u563.toulouse.inserm.fr/">http://www.u563.toulouse.inserm.fr/</a></span></font></address></div>_______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></div></span></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Ensembl Bioinformatician,</div></div><div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span> </div><br></div></body></html>