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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">Dear <span class="highlight" id="0.9645808873867432" name="searchHitInReadingPane" style="background-color: rgb(255, 255, 255);">BioPerl</span><span style="background-color: rgb(255, 255, 255);"> </span>community,</p>
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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">I am trying to use <a href="http://recode.ucc.ie/oaf/" target="_blank">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" target="_blank">here</a>. I installed Perl (v5.22.2) and <span class="highlight" id="0.2166116948116641" name="searchHitInReadingPane" 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" target="_blank">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" target="_blank" title="http://recode.ucc.ie/oaf/download
Ctrl+Click or tap to follow the link">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" name="searchHitInReadingPane" 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;">-
<b><u>BPbl2seq</u></b> -</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"><span style="font-size: 16px;">BPbl2seq</span></font>. </p>
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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;"><span style="font-size: 12pt;">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>
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<div style="margin-top: 0px; margin-bottom: 0px;">I look forward to hearing from you.<br>
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<div style="margin-top: 0px; margin-bottom: 0px;">Thank you and kind regards,<br>
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<div style="margin-top: 0px; margin-bottom: 0px;">Jernej Turnsek</div>
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<div><span style="color:rgb(34,34,34)"><font size="1" face="Arial"><b>Jernej Turnsek </b></font></span></div>
<div style="font-size:small"><span style="font-family:Arial; font-size:x-small"><font color="#222222">Ph.D. Candidate |
</font><a href="https://silver.med.harvard.edu/" id="LPNoLP"><font color="#0000ff">Pamela Silver's Lab </font></a></span></div>
<div style="font-size:small"><span style="font-size:x-small; color:rgb(34,34,34)"><font face="Arial">Department of Systems Biology | Harvard Medical School</font></span></div>
<div style="font-size:small"><span style="font-size:x-small; color:rgb(34,34,34)"><font face="Arial">200 Longwood Ave | Boston, MA 02115</font></span></div>
<div style="font-size:small"><font size="1" style="font-family:Arial"><font color="#222222">(617) 797-5386 |
</font><a href="http://openwetware.org/wiki/User:JernejTurnsek" id="LPNoLP"><font color="#0000ff">Web</font></a><font color="#222222"> |
</font></font><span style="font-family:Arial; font-size:x-small"><a href="https://www.linkedin.com/in/jernejt" id="LPNoLP"><font color="#0000ff">LinkedIn</font></a> </span><span style="font-family:Arial; font-size:x-small">|
<font color="#0000ff"><a href="https://twitter.com/" id="LPNoLP">@SynEnthu</a></font></span></div>
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