SYEH@BIONET-20.BIO.NET (Spencer Yeh) (12/01/88)
Dear Bionet Users,
Donald Roufa and Douglas Rhoads have supplied BIONET with an updated
version of their SEQAID II PC program for DNA and protein sequence
analysis for inclusion in the BIONET Lending Library of contributed
software. Version 3.10 is a minor modification of version 3.0 that
has alterations to the module which locates reading frames by codon bias.
Slight changes have been made to the calculation of frame probability
scores which, in most cases, do not affect the interpretation of
results. The output has also been clarified and the literature
reference included for this module.
Below I'm including information about version 3.0 which still applies
to version 3.1, and information for obtaining this public domain
software.
Sincerely,
Spencer Yeh Internet: bionet@bionet-20.bio.net
Applications Analyst (for BIONET issues)
BIONET
(415) 324-4363
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Some of the NEW features of version 3.0 include:
1. The capability of extracting sequences out of a GenBank floppy disk
release. (GenBank must be obtained separately).
2. A very nice module for creating codon bias tables from a set of
exons or cDNAs, and then using the codon bias tables to look
for possible coding regions in DNA sequences. This module
creates codon bias tables in human-readable form, as well as in
the computer-readable form needed by the program.
The infomation appended below is from the on-line help topic HELP
SEQAID contained in the file BC:SEQAID.HLP on BIONET:
SEQAID II (version 3.0)
September 1988 Donald Roufa and D.D. Rhoads
("readme.doc" added 9/14/88 by Spencer Yeh)
INTRODUCTION
SEQAID II is a multifunctional PC program for DNA and protein sequence
analysis. Functions include editing, extracting sequences from a
GenBank floppy disk release (not provided), dot matrix comparison,
fragment sizer, base composition, translations, protein structure and
hydropathicity, restriction site search, and locating potential exons
by codon bias.
CONTACT ADDRESS
For questions about the program or suggestions for future improvements
please contact:
Donald J. Roufa and D.D. Rhoads
Division of Biology
Ackert Hall
Kansas State University
Manhattan, KS 66506
tel.: (913) 532-6641
e-mail: droufa@ksuvm.ksu.edu
or droufa@bionet-20.bio.net
SYSTEMS SUPPORTED
An IBM-compatible computer running MS-DOS (2.1 or greater) is needed.
The program requires at least 175K internal memory for the program plus
space for sequence files. A total of 640K should be sufficient for
most users.
AVAILABILITY
SEQAID II is available from the BIONET Lending Library. Please send a
stamped, self-addressed return envelope along with a formatted MS-DOS
diskette (5 1/4" or 3 1/2") with your request to:
BIONET Administrator
700 East El Camino Real
Mountain View, CA 94040
tel.: (415) 962-7300
DISKETTE FILES
README.DOC This documentation file
SEQAIDFD.EXE Self-extracting archive of SEQAID II files
SEQAIDII.NEW Release notes for version 3.0
INSTALL.DOC Installation instructions
STARTING THE PROGRAM
Please read the file INSTALL.DOC for installation instructions. The
SEQAID II package must be first de-archived. Once the files are
successfully dearchived, the user manual for SEQAID will be found in the
"README" file.
It is recommended that the user copy the program files to hard disk so
that more disk space will be available to the program.
RELEASE NOTES FOR VERSION 3.0 ("SEQAIDII.NEW")
S E Q A I D I I Version 3.0
============================
D.D. Rhoads and D.J. Roufa
Division of Biology
Kansas State University
An upgraded release of the SEQAIDII DNA Sequence analysis
software package has been posted in the BIONET Software Lending
Library. Version 3.0, contains several new modules and enhanced
functions. In addition, a couple of subtle malfunctions in the code
(bugs??) have been corrected.
New features include a gateway to the GenBank database (floppy disk
release) and a user-friendly interface to search and extract genetic data
from the database. As supplied, SEQAIDII accesses floppy disk versions of
GenBank, Release 55.0 and earlier. Included is a utility, GBHEADER.EXE,
which permits users to modify the GenBank format file, HDR550.GBK, to
accomodate future floppy disk releases. As implemented, SEQAIDII accesses
floppy disk releases of GenBank either segmented on diskettes or combined
in a subdirectory of the user's harddisk.
SEQAIDII version 3.0 contains a new module that scans anonymous
nucleic acid sequences for potential protein coding regions based upon
codon useage frequencies. The module permits the user to construct and
amplify required codon bias tables from appropriate nucleic acid sequences
(cDNAs or spliced exon sequences) and to save the tables to disk. SEQAIDII
suggests a default filename (CODON.USE) for codon bias table files; but
the user can accumulate multiple codon bias table files (perhaps one for
each species of interest) by specifying a unique filename for each.
Version 3.0 now can be customized to implement variant genetic
codes, such as used in mitochondrial DNAs, to alter amino acid one- and
three-letter abbreviations, and to edit values for amino acid residue
physical data used to generate hydropathicity and antigenicity plots,
reverse translations, and polypeptide molecular weights. Enhanced features
include the ability to view ASCII data disk files from within the SEQAIDII
environment and customization of the sequence entry interface.
SEQAIDII version 3.0 is supplied as a self-extracting archive file,
SEQAIDFD.EXE (for GenBank 'F'loppy 'D'isk releases). When GenBank
implements a CD-ROM release format, as currently being planned, the authors
will post a version of SEQAIDII that accomodates the new GenBank database
format (SEQAIDCD.EXE). Watch for future announcements regarding the
availability of SEQAIDCD.EXE.
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