[Bioperl-l] Cannot download/find BPbl2seq module

[Turnsek, Jernej]

Dear BioPerl community,


I am trying to use OAF<http://recode.ucc.ie/oaf/> - 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 here<http://www.ncbi.nlm.nih.gov/pubmed/18384676>. 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 (see this link<http://recode.ucc.ie/oaf/download>). What I tried to do next is replicate the "my_sequence" example listed on this website<http://recode.ucc.ie/oaf/download> using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - 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 BPbl2seq.


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.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek



Jernej Turnsek
Ph.D. Candidate | Pamela Silver's Lab <https://silver.med.harvard.edu/>
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web<http://openwetware.org/wiki/User:JernejTurnsek> | LinkedIn<https://www.linkedin.com/in/jernejt> | @SynEnthu<https://twitter.com/>
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