<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" 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 BioPerl 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;">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 BioPerl (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" target="_blank" title="http://recode.ucc.ie/oaf/download
Ctrl+Click or tap to follow the link">this website</a> using the attached oaf.pl
script and .fasta file, but ended up stuck with the message you can also find attached. It looks like I am missing a necessary BioPerl module <span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;">-
Bio::Tools:BPbl2seq -</span> which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. </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 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;"><span style="font-size: 12pt;">Thank you and kind regards,</span><br>
</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;">Jernej Turnsek</p>
<br>
<p></p>
<p><br>
</p>
<div id="Signature">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-size:13px">
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div style="background-color:rgb(255,255,255)">
<div style="font-size:small"><br>
</div>
<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">|
<a href="https://twitter.com/" id="LPNoLP"><font color="#0000ff">@SynEnthu</font></a></span></div>
</div>
<div style="font-size:small; background-color:rgb(255,255,255)"></div>
</div>
<div style="font-size:13px">
<div style="color:rgb(34,34,34); background-color:rgb(255,255,255)"><br>
</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>
</body>
</html>