Local Software Documentation

• ACEDB, the database for C. elegans genetics.
  There is a host of documentation on the Natation Agricultural Library web server, the ANGIS manual is recommended.

  BioMotif a tool for identifying user definable motifs in DNA or protien sequences.

  Be sure to look at the Simple Example page, as it tells you where the bioMotif library files are located.

  Boxshade

  This program is used with multple sequence alignments to produce a postscript file with character shading.

  hmmer

  Biological sequence analysis using profile hidden Markov models, from Washington U., St. Louis.

  Genefinder, A note about starting to use genefinder, and the main documentation file.

  Genefinder, like XGrail, is a program to identify genes in a DNA sequence. However, genefinder runs locally on this computer.

  XGrail setup and the users guide.

  XGrail is client software which allows one to send a DNA sequence to the Oak Ridge Lab and receive back putative gene features.