<p dir="ltr">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>
Mark</p>
<div class="cm_quote" style=" color: #787878">On Wed, May 25, 2016 at 1:21
PM, Turnsek, Jernej <<a
href="mailto:turnsek@fas.harvard.edu">turnsek@fas.harvard.edu</a>>
wrote:</div><br><div id="oldcontent" style="background: rgb(255, 255,
255);"><blockquote style="">
<style style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
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style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p></p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;">Dear <span class="highlight" id="0.9645808873867432"
style="background-color: rgb(255, 255, 255);">BioPerl</span><span
style="background-color: rgb(255, 255, 255);"> </span>community,</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;"><br>
</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;"></p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;">I am trying to use <a
href="http://recode.ucc.ie/oaf/">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">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">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">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;">-
<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>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;"><span style="font-size: 12pt;"><br>
</span></p>
<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>
<p></p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;"><br>
</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;"></p>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size:
16px;">
<div id="divtagdefaultwrapper"><font
face="Calibri,Arial,Helvetica,sans-serif">
<div style="margin-top: 0px; margin-bottom: 0px;">I look forward to hearing
from you.<br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">Thank you and kind
regards,<br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<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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