[Bioperl-l] Bio::Tools::Genewise

Jason Stajich jason at cgt.duhs.duke.edu
Fri Mar 19 12:14:02 EST 2004

I think it is 2.2.0.  Note the ! lines.

For those of you on linux biolinux.org provides a nice rpm install of wise

[jason at lugano jason]$ genewise -help
genewise ($Name: wise2-2-0 $)
genewise <protein-file> <dna-file> in fasta format
Dna sequence options
  -u               start position in dna
  -v               end position in dna
  -trev            Compare on the reverse strand
  -tfor [default]  Compare on the forward strand
  -both            Both strands
  -tabs            Report positions as absolute to truncated/reverse
  -fembl            File is an EMBL file native format
Protein comparison options
  -s               start position in protein
  -t               end   position in protein
  -[g]ap    [ 12]  gap penalty
  -[e]xt    [  2]  extension penalty
  -[m]atrix [blosum62.bla]  Comparison matrix
HMM options
  -hmmer           Protein file is HMMer file (version 2 compatible)
  -hname           Use this as the name of the HMM, not filename
Gene Model options
  -init   [default]  [default/global/local/wing/endbias] startend policy
for the HMM/protein
  -codon  [codon.table]  Codon file
  -gene   [human.gf]  Gene parameter file
  -subs   [1e-05] Substitution error rate
  -indel  [1e-05] Insertion/deletion error rate
  -cfreq  [model/flat] Using codon bias or not?     [default flat]
  -splice [model/flat] Using splice model or GT/AG? [default model]
  -intron [model/tied] Use tied model for introns   [default tied]
  -null   [syn/flat]   Random Model as synchronous or flat [default syn]
  -pg     <file>       Potential Gene file (heurestic for speeding
  -alln   [1.0]   Probability of matching a NNN codon
  -insert [model/flat] Use protein insert model     [default flat]
Algorithm options
  -alg    [623/623L/2193/2193L]  Algorithm used [default 623/623L]
Output options [default -pretty -para]
  -pretty          show pretty ascii output
  -pseudo          Mark genes with frameshifts as pseudogenes
  -genes           show gene structure
!  -genesf          show gene structure with supporting evidence
   -embl            show EMBL feature format with CDS key
  -diana           show EMBL feature format with misc_feature key (for
  -para            show parameters
  -sum             show summary output
  -cdna            show cDNA
  -trans           show protein translation, breaking at frameshifts
  -pep             show protein translation, splicing frameshifts
  -ace             ace file gene structure
  -gff             Gene Feature Format file
  -gener           raw gene structure
  -alb             show logical AlnBlock alignment
  -pal             show raw matrix alignment
  -block  [50]     Length of main block in pretty output
  -divide [//]     divide string for multiple outputs
New gene model statistics
  -splice_max_collar      [5.0]  maximum Bits value for a splice site
  -splice_min_collar      [-5.0] minimum Bits value for a splice site
  -splice_score_offset    [4.5]  score offset for splice sites
  -genestats              [gene.stat]
Dynamic programming matrix implementation
  -dymem      memory style [default/linear/explicit]
  -kbyte      memory amount to use [4000]
  -dydebug    drop into dynamite dp matrix debugger
Standard options
  -help      help
  -version   show version and compile info
  -silent    No messages on stderr
  -quiet     No report on stderr
  -erroroffstd No warning messages to stderr
  -errorlog [file] Log warning messages to file

See WWW help at http://www.sanger.ac.uk/Software/Wise2/

On Fri, 19 Mar 2004, Ewan Birney wrote:

> On Thu, 18 Mar 2004, Shawn Hoon wrote:
> > You would need to add the -genesf option when running genewise.
> >
> > Also, you can check out the wrapper for genewise in
> > Bio::Tools::Run::Genewise in the bioperl-run package.
> I think -genesf is only available in the (now rather venerable) release
> candidate Genewise at
> http://www.sanger.ac.uk/Users/birney/wise2.2.3-rc7.tar.gz
> The reason for not releasing this is that actually I need to back out the
> changes made for the case of BLOSUM62.bla (it is in fact better to keep as
> backwardly compatible as possible) which all comes down to the case
> insanity that is Apple's HFS+ file system not playing nicely with cvs.
> (yup. That was too much detail right?)
> I will try to push the Wise2 package into some sort of sanity over this
> month wrt to these things and then make a proper release. For the moment,
> use the release candidate above...
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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