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Appendix A: How to get Genotator and the programs it uses

Genotator is available free of charge to non-profit institutions only. For information on obtaining it, please write to the author (nlharris@lbl.gov). Genotator runs on Unix workstations; it has been tested on Suns (running Solaris 1 or 2), SGIs, and DEC Alphas. The browser is straightforward to install offsite; the back end is more complex because it expects to find the various sequence analysis tools (BLAST, gene finders, etc.), some of which are not available offsite. The back end is set up so that it can run with any subset of the analysis tools it is expecting, but if you're missing most of them, the results won't be very interesting.

System requirements

Browser requires:

• Perl 5.002 or higher
  Get from ftp://ftp.digital.com/pub/plan/perl/CPAN/src/5.0/perl5.003.tar.gz
• Tkperl (Tk-b3 or higher)
  "This package is free software; you can redistribute it and/or modify it under the same terms as Perl itself, with the excepton of all the files in the pTk sub-directory which have separate terms derived from those of the orignal Tk4.0 sources. See pTk/license.terms for details of this license."
  Get from ftp://ftp.rge.com/pub/languages/perl/authors/id/NI-S/

Optional:

• blixem (for displaying GenPept blast hits):
  Get from ftp://ftp.sanger.ac.uk/pub/MSPcrunch/
• Primer3:
  http://www-genome.wi.mit.edu/genome_software/other/primer3.html
• process-hits and process-blast.pl (by Nomi)
  Included in Genotator distribution.

  Genotator uses:

  (Note: all of these are optional; if you're missing one of them, Genotator will leave that row blank, or, in some cases, leave out the row. But it's not really worth your while to run Genotator if you can't get most of these sequence analysis programs set up at your site.)

  Gene finders:

  • GRAIL:
    ftp://arthur.epm.ornl.gov/pub/grailclnt/[dec/sgi/sun]
  • Genefinder:
    or email Colin Wilson (colin@genes.biotech.washington.edu)
    ftp://ftp.genome.washington.edu/src/ (you need the genefinder, libutil, and tables tar files). [I couldn't get them to compile on my system the last time I tried.]
  • xpound:
    email alun@myriad.com
  • GeneMark:
    email James McIninch (james@amber.biology.gatech.edu)
  • Genie:
    David Kulp and Martin Reese [Not yet available offsite]

  My scripts:

  • find-start-and-stop
  • process-hits
    • process-blast.pl
  • parse-genemark
  • parse-gf
  • parse-gf-for-orfs
  • parse-grail
  • parse-xpound
  • parse-genie
  • process-signals
    • process-promoters.pl

  Other programs:

  • MSPcrunch:
    Get from ftp://ncbi.nlm.nih.gov/pub/esr/MSPcrunch+Blixem.
  • tRNAscan:
    ftp://genome.wustl.edu/pub/eddy/tRNAscan-SE-0.96a.tar.Z
    [Genotator runs this but since it almost never finds anything I don't bother making the browser display it.]
  • gb2fasta (from NCBI): Executables are in ftp://ncbi.nlm.nih.gov/blast/executables/ (look for the subdirectory for your operating system).
  • blastn, blastx (from NCBI): Source code is at ftp://ncbi.nlm.nih.gov/. Executables are in ftp://ncbi.nlm.nih.gov/blast/executables/ (look for the subdirectory for your operating system). This is probably your better bet, as compiling NCBI programs is complicated.
  • xblast: ftp://ncbi.nlm.nih.gov/pub/jmc/xblast/
  • seqsplit, blastunsplit (from Sanger) (but I have hacked versions of these)
  • Martin Reese's programs:
    Not currently available offsite, but you can try contacting Martin at mgreese@lbl.gov.
    
  • BLASTable databases:
    • EST database (NCBI):
      ftp://ncbi.nlm.nih.gov/genbank/gbest*.seq.Z
      Download all of them (this takes a while!) compress each one, run gb2fasta on each piece, cat together all of the FASTA format pieces, then run pressdb (available in ftp://ncbi.nlm.nih.gov/blast/executables/) to make a blastable database.
    • GenPept (NCBI):
      ftp://ncbi.nlm.nih.gov/genbank/genpept.fsa.Z
      (Uncompress and use setdb to make a blastable database.)
    • Repeats databases:
      
      • Human: http://www-hgc.lbl.gov/inf/genotator/repeat-dbs/humrep
      • Invertebrate: http://www-hgc.lbl.gov/inf/genotator/repeat-dbs/invrep

  

  Figure 5: The Genotator browser map display of the annotations on HUMTFPB.

  The default annotation colors are:

  Magenta	NNPP promoter predictions
  Red	GenPept hits (using BLASTX): GenPept consists of all the GenBank coding regions translated to amino acids
  Orange	EST hits (using BLASTN)
  Yellow	Human repeat sequence hits (using BLASTN)
  Chartreuse	xpound exon predictions
  Green	GeneFinder exon predictions
  Turquoise	GRAIL exon predictions
  Dark Blue	Genie exon predictions
  Purple	GenBank CDS (exons)
  Magenta/Red/Orange	Open reading frames (>=150 bases), colored by frame

  

  Figure 6: The Genotator browser sequence display showing the sequence of HUMTFPB. The user has clicked on a GenPept BLAST hit in the map display, causing the corresponding sequence region to be highlighted in red in the sequence display.

  

  Figure 8: Annotations on h78_1_c10, indicating a possible new gene associated with the photoreceptor membrane.

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