<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Mark,</div><div class=""><br class=""></div>Bio::Tools::BPbl2seq was a part of the BLAST parsing BPLite package, written by Ian Korf way back when. BPLite was removed from Bioperl some years ago.<div class=""><br class=""></div><div class="">Brian O.<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 25, 2016, at 3:12 PM, Mark A Jensen <<a href="mailto:maj@fortinbras.us" class="">maj@fortinbras.us</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><p dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Oops, I am wrong about this.<span class="Apple-converted-space"> </span><br class="">There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the<span class="Apple-converted-space"> </span><a href="http://module.is/" class="">module.is</a><span class="Apple-converted-space"> </span>present but contains a syntax error.</p><div class="cm_quote" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; color: rgb(120, 120, 120);">On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <<a href="mailto:maj@fortinbras.us" class="">maj@fortinbras.us</a>> wrote:</div><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div id="oldcontent" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><blockquote class=""><p dir="ltr" class="">Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"<br class="">Mark</p><div class="cm_quote" style="color: rgb(120, 120, 120);">On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <<a href="mailto:turnsek@fas.harvard.edu" class="">turnsek@fas.harvard.edu</a>> wrote:</div><br class=""><div id="oldcontent" style="background-color: rgb(255, 255, 255); background-position: initial initial; background-repeat: initial initial;" class=""><blockquote class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div class=""><br class="webkit-block-placeholder"></div><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">Dear <span class="highlight" id="0.9645808873867432" style="background-color: rgb(255, 255, 255);">BioPerl</span><span style="background-color: rgb(255, 255, 255);" class=""> </span>community,</p><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><br class=""></p><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><br class="webkit-block-placeholder"></div><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">I am trying to use <a href="http://recode.ucc.ie/oaf/" class="">OAF</a> - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available <a href="http://www.ncbi.nlm.nih.gov/pubmed/18384676" class="">here</a>. I installed Perl (v5.22.2) and <span class="highlight" id="0.2166116948116641" style="background-color: rgb(255, 255, 255);">BioPerl</span> (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (<a href="http://recode.ucc.ie/oaf/download" class="">see this link</a>). What I tried to do next is replicate the "my_sequence" example listed on <a href="http://recode.ucc.ie/oaf/download" title="http://recode.ucc.ie/oaf/download
Ctrl+Click or tap to follow the link" class="">this website</a> using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary <span class="highlight" id="0.6919624283748245" style="background-color: rgb(255, 255, 255);">BioPerl</span> module <span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class="">-<span class="Apple-converted-space"> </span><b class=""><u class="">BPbl2seq</u></b><span class="Apple-converted-space"> </span>-</span> which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including <font face="Calibri,Arial,Helvetica,sans-serif,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols" size="2" class=""><span style="font-size: 16px;" class="">BPbl2seq</span></font>. </p><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><span style="font-size: 12pt;" class=""><br class=""></span></p><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><span style="font-size: 12pt;" class="">I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.</span></p><div class=""><br class="webkit-block-placeholder"></div><p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><br class=""></p><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><br class="webkit-block-placeholder"></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><div id="divtagdefaultwrapper" class=""><font face="Calibri,Arial,Helvetica,sans-serif" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">I look forward to hearing from you.<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you and kind regards,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Jernej Turnsek</div></font></div></div><div class=""><br class="webkit-block-placeholder"></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class=""><br class="webkit-block-placeholder"></div><br class=""><div class=""><br class="webkit-block-placeholder"></div><p class=""><br class=""></p><div id="Signature" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-size: 13px;" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div style="background-color: rgb(255, 255, 255);" class=""><div style="font-size: small;" class=""><br class=""></div><div class=""><span style="color: rgb(34, 34, 34);" class=""><font size="1" face="Arial" class=""><b class="">Jernej Turnsek </b></font></span></div><div style="font-size: small;" class=""><span style="font-family: Arial; font-size: x-small;" class=""><font color="#222222" class="">Ph.D. Candidate |<span class="Apple-converted-space"> </span></font><a href="https://silver.med.harvard.edu/" id="LPNoLP" class=""><font color="#0000ff" class="">Pamela Silver's Lab </font></a></span></div><div style="font-size: small;" class=""><span style="font-size: x-small; color: rgb(34, 34, 34);" class=""><font face="Arial" class="">Department of Systems Biology | Harvard Medical School</font></span></div><div style="font-size: small;" class=""><span style="font-size: x-small; color: rgb(34, 34, 34);" class=""><font face="Arial" class="">200 Longwood Ave | Boston, MA 02115</font></span></div><div style="font-size: small;" class=""><font size="1" style="font-family: Arial;" class=""><font color="#222222" class="">(617) 797-5386 |<span class="Apple-converted-space"> </span></font><a href="http://openwetware.org/wiki/User:JernejTurnsek" id="LPNoLP" class=""><font color="#0000ff" class="">Web</font></a><font color="#222222" class=""><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span></font></font><span style="font-family: Arial; font-size: x-small;" class=""><a href="https://www.linkedin.com/in/jernejt" id="LPNoLP" class=""><font color="#0000ff" class="">LinkedIn</font></a> </span><span style="font-family: Arial; font-size: x-small;" class="">|<span class="Apple-converted-space"> </span><font color="#0000ff" class=""><a href="https://twitter.com/" id="LPNoLP" class="">@SynEnthu</a></font></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div></blockquote></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; 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