What Is In The Individual Information Program Package?

• The Individual information program package consists of an entire directory containing programs and files ready to run. The programs are available only through agreements with NIH .

• The individual information and walker software are provided as Sun Microsystems Sparc binaries for Solaris 2.6. Obtaining the Pascal source code is negotiable under the terms of a license agreement.
  • Under license depending on the agreement:
    • Sparc Binaries
    • Sparc Binaries + source code
  • Under MTA (within NIH):
    • Sparc Binaries, no expiration date
  • Under CDS (outside NIH for research/eduational):
    • Sparc Binaries with expiration date

• Step-by-step instructions for using the programs will be provided when you obtain them. To use them effectively, you will need to be familiar with the theory.
  • To learn basic information theory, see the Primer on Information Theory.
  • To learn the individual information theory, see the papers listed at the page on walkers.

• Manual pages are now available online for each program. The manual pages can be accessed by a web browser. The format follows that of the shell program.

• Demonstration Unix shell scripts are included in the package:
  • libdef.test - tests extraction and mutation of DNA sequences
  • logowalker.test - tests the generation of sequence logos and sequence walkers.
  • plot.test - run in conjunction with logowalker.test, this makes both dnaplot and xyplo graphs.
  • splice.test - tests analysis of mutations at splice junctions
  • mfold.test - tests analysis of mutations at splice junctions in conjunction with mRNA structure
  These scripts contain every step necessary to do the analysis, so by looking at them and copying and modifying them for your own purposes, you should be able to do the same analyses on your own sequences. The demonstrations start from GenBank flat files that are included in the package.

• Standardized analyses are now available:
  • run.logo - creates a sequence logo and a ribl matrix
  • run.splice - does splice junction analysis
  • run.mfold - does mRNA folding

• All necessary parameter files are supplied in the package. This means that there are working examples to start from. All parameters are described in detail in the manual page and often in a short notation in the parameter file. Parameter files are in ASCII (text), which means that they can be easily modified with an editor or by a program. This also allows one to construct graphical user interfaces such as weblogo on top of the system.

• All programs needed for the demonstrations are included in the package, but some of these are publically available. Publically available Delila programs are described at http://www.lecb.ncifcrf.gov/~toms/delila.html and are listed at http://www.lecb.ncifcrf.gov/~toms/delila/delilaprograms.html.

• There is a test program which you can use to see if you are able to use the binaries or the source code.

• The entire package currently takes about 36 MegaBytes.

• For information about how to obtain these programs, please contact us.

Schneider Lab
origin: 1998 February 26
updated: 2000 June 15