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

[Edward Chuong]

> > 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!
-- 
Edward Chuong
http://iacs5.ucsd.edu/~echuong