[Bioperl-l] Help on a basic EST-genomic alignment script

[Jason Stajich]

Just use estwise as a standalone program not from within perl.
 % estwise protein est

estwise is pretty slow so I wouldn't embark on this route unless you know
what you are doing.  Try a BLAST or FASTA route first to get likely
homologs.

I would probably start with fastx or fasty first to find likely homologs
and get a good guess about the reading frame.  fastx and fasty are
translated search algorithms (analagous blastx). From the docs

fastx3/ fasty3     Compare a DNA sequence to a protein sequence  database,
                   by  comparing  the  translated  DNA  sequence  in three
                   frames and allowing gaps and frameshifts.  fastx3  uses
                   a  simpler, faster algorithm for alignments that allows
                   frameshifts only between codons; fasty3 is  slower  but
                   produces  better alignments with poor quality sequences
                   because frameshifts are allowed within codons.

This should have come on the BioTeam installer in the fasta pkg.

-jason

On Mon, 28 Jun 2004, Edward Chuong wrote:

> > > You basically need to predict the protein sequence from the EST - you can
> > > use estwise to do this based on the best mouse protein homolog.
> >
>
> Hey,
>
> I just downloaded estwise and it works much better than clustalw for
> est alignment. How do I use this from perl? I'm having trouble
> installing the perl module for it (make perl ?) wise2.2.0.. I had to
> use the BioTeam OS X pkg to install the binaries (binaries worked fine
> for testing but obvoiusly I need to access estwise from perl!). I get
> the following errors trying to compile from source (tried with su as
> well) on OS X 10.3.4.
>
> ld: Undefined symbols:
> _HMMFileOpenFseek
> _HMMFtell
> _ajCharNewL
> _ajMemCalloc0
> _ajSeqChar
> _ajSeqsetFill
> _ajSeqsetGetFormat
> _ajSeqsetGetSeq
> _ajSeqsetIsDna
> _ajSeqsetIsProt
> _ajSeqsetIsRna
> _ajSeqsetLen
> _ajSeqsetName
> _ajSeqsetSize
> _ajSeqsetToUpper
> _ajSeqsetWeight
> _ajStrLen
> _ajStrPrefixC
> _ajStrStr
> _ajMessCrashFL
> _ajMessSetErr
> _ajFmtPrintF
> make[1]: *** [estwise] Error 1
> make: *** [realall] Error 2
>
> Then running "make perl" (which probably shouldn't work anyway because
> the original compile didn't) I get:
>
> /usr/bin/perl /System/Library/Perl/5.8.1/ExtUtils/xsubpp  -typemap
> /System/Library/Perl/5.8.1/ExtUtils/typemap -typemap typemap  Wise2.xs
> > Wise2.xsc && mv Wise2.xsc Wise2.c
> Error: 'Wise2_SupportingFeature *' not in typemap in Wise2.xs, line 6081
> Error: 'Wise2_SupportingFeature *' not in typemap in Wise2.xs, line 6108
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 6650
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 6710
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 6730
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 8322
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 8337
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 8352
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 8368
> Error: 'Wise2_DPRunImpl *' not in typemap in Wise2.xs, line 8384
> make[1]: *** [Wise2.c] Error 1
> make: *** [perlmake] Error 2
>
> Anyone out there with experience installing wise in OS X?
>
> Thanks!
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu