<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear All,<div><br><div>I have downloaded the PFAM full list for mm9 and would like to obtain the genomic coordinates for each record (from cols 2+3 below )</div><div><br></div><div>Is there someone with recyclable code for doing so?</div><div><br></div><div>My input is in Swissprot format (relative to ATG in the relative Acc as shown below</div><div></div><blockquote type="cite"><div>
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<td height="15" colspan="8" width="520" style="height:15.0pt;mso-ignore:colspan;
width:520pt">#Pfam-A regions from Pfam version 26.0 for ncbi taxid 10090 'Mus
musculus (strain C57BL/6)'</td>
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<td height="15" colspan="4" style="height:15.0pt;mso-ignore:colspan">#Total
number of proteins in proteome: 47211</td>
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<td height="15" colspan="14" style="height:15.0pt;mso-ignore:colspan">#<seq
id> <alignment start> <alignment end> <envelope start>
<envelope end> <hmm acc> <hmm name> <type> <hmm
start> <hmm end> <hmm length> <bit score>
<E-value> <clan></td>
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<td height="15" style="height:15.0pt">Q9JKB1</td>
<td align="right">5</td>
<td align="right">215</td>
<td align="right">5</td>
<td align="right">216</td>
<td>PF01088</td>
<td>Peptidase_C12</td>
<td>Domain</td>
<td align="right">1</td>
<td align="right">213</td>
<td align="right">214</td>
<td>271.10</td>
<td>4.6e-78</td>
<td>CL0125</td>
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<td height="15" style="height:15.0pt">E9Q751</td>
<td align="right">46</td>
<td align="right">129</td>
<td align="right">46</td>
<td align="right">129</td>
<td>PF04822</td>
<td>Takusan</td>
<td>Family</td>
<td align="right">1</td>
<td align="right">84</td>
<td align="right">84</td>
<td>96.90</td>
<td>4.5e-25</td>
<td>No_clan</td>
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<td height="15" style="height:15.0pt">D3YVR1</td>
<td align="right">2</td>
<td align="right">161</td>
<td align="right">2</td>
<td align="right">161</td>
<td>PF00743</td>
<td>FMO-like</td>
<td>Family</td>
<td align="right">1</td>
<td align="right">160</td>
<td align="right">532</td>
<td>325.60</td>
<td>4.1e-94</td>
<td>CL0063</td>
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<td height="15" style="height:15.0pt">B1AQR8</td>
<td align="right">223</td>
<td align="right">351</td>
<td align="right">223</td>
<td align="right">352</td>
<td>PF00337</td>
<td>Gal-bind_lectin</td>
<td>Domain</td>
<td align="right">1</td>
<td align="right">132</td>
<td align="right">133</td>
<td>134.30</td>
<td>1.6e-36</td>
<td>CL0004</td>
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</tbody></table></div></blockquote><div><br></div><div>this looks feasible and probably needs some external ref and slice magic, I have not used this for several years now and am a bit rusted</div><div><br></div><div>Thanks for any piece of code to start with</div><div><br></div><div>Stephane</div></div></body></html>