<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Daniel,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>have a look at iprscan, which is a very complete tool:</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> <A href="http://www.ebi.ac.uk/InterProScan/">http://www.ebi.ac.uk/InterProScan/</A></DIV><DIV>For command-line access, see:</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> <A href="http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html">http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html</A></DIV><DIV>You can also set it up locally.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>For each protein, the output is one line per domain found on that protein.</DIV><DIV>I concatenate the output files into one big file, and then count the different domains I have.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Best,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>yannick<BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 11px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">___________________________________</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:yannick.wurm@unil.ch"><FONT class="Apple-style-span" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(0, 0, 238); -khtml-text-decorations-in-effect: underline; "><SPAN class="Apple-style-span" style="color: rgb(0, 0, 238); font-size: 10px; -khtml-text-decorations-in-effect: underline; ">yannick.wurm@unil.ch</SPAN></SPAN></FONT></A><FONT class="Apple-style-span" color="#001B7A" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(0, 27, 122); "><SPAN class="Apple-style-span" style="color: rgb(0, 27, 122); font-size: 10px; "> </SPAN></SPAN></FONT><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; "> - Doctoral student</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">Department of Ecology and Evolution </SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.unil.ch/dee/page28685.html"><FONT class="Apple-style-span" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(0, 0, 238); -khtml-text-decorations-in-effect: underline; "><SPAN class="Apple-style-span" style="color: rgb(0, 0, 238); font-size: 10px; -khtml-text-decorations-in-effect: underline; ">http://www.unil.ch/dee/page28685.html</SPAN></SPAN></FONT></A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Lucida Grande; min-height: 12px; ; font-size: 10px; "><BR style="font-size: 10px; "></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">#3106, Biophore, Universite de Lausanne</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">1015 Lausanne, Switzerland</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">land: +41.21.692.4182 fax: +41.21.692.4165</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#747B7B" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;; color: rgb(116, 123, 123); "><SPAN class="Apple-style-span" style="color: rgb(116, 123, 123); font-size: 10px; ">cell: +41.78.87.87.001</SPAN></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 11px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "></SPAN><BR class="Apple-interchange-newline"></SPAN> </DIV><BR><DIV><DIV>On 5 juin 06, at 12:00, <A href="mailto:bio_bulletin_board-request@bioinformatics.org">bio_bulletin_board-request@bioinformatics.org</A> wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Lucida Grande; min-height: 13.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Lucida Grande; min-height: 13.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">I am after a way in which I can analyze large data sets of protein<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">sequences, where the readout is a quantification of different protein<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">domains that are found within a given list of sequences (e.g. a list of<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">500 protein sequences in FASTA format).<SPAN class="Apple-converted-space"> </SPAN>Preferably the output would be<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">at the systems level (e.g. 230 Tyrosine Kinase domains) rather than that<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">describing domains only at a protein-by protein level.</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Lucida Grande; min-height: 13.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">Thanks,</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Lucida Grande; min-height: 13.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">Daniel</FONT></P> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>