STONE@yalemed.bitnet (05/16/89)
IBM/McIntosh computer programs for molecular biology (freeware)
The following computer programs for molecular biologists are available
from:
Hal B. Jenson, M.D.
Department of Pediatrics
Yale University School of Medicine
333 Cedar Street
New Haven, CT 06410
Indicate the programs desired and the computer format (IBM or
McIntosh). Please enclose $5.00 to cover the expense of the discs and
mailing costs.
Program: CLONES
Reference: BioTechniques vol. 7, June 1989
A novel computer database program dedicated to storing, cataloging,
and accessing information about recombinant clones and libraries has
been developed for the IBM (or compatible) personal computer. This
program, named CLONES, also stores information about bacterial strains
and plasmid and bacteriophage vectors used in molecular biology. The
advantages of this method are improved organization of data, fast and
easy assimilation of new data, automatic association of new data with
existing data, and rapid retrieval of desired records using search
criteria specified by the user. Individual records are indexed in the
database using B-trees, which automatically index new entries and
expedite later access. The use of multiple windows, pull-down menus,
scrolling pick-lists, and field-input techniques make the program
intuitive to understand and easy to use. Daughter databases can be
created to include all records of a particular type, or only those
records matching user-specified search criteria. Separate databases
can also be merged into a larger database. This computer program
provides an easy-to-use and accurate means to organize, maintain,
access, and share information about recombinant clones and other
laboratory products of molecular biology technology.
Requirements: IBM PC/XT/AT/PS2 or compatible
DOS 2.1 or above
256 Kb available RAM
Program: LIGATE
Reference: BioTechniques 5:729-730, 1987
Description: A computer program to facilitate determination of the
amounts of vector DNA and insert DNA for a given set of ligation
reaction conditions. The desired conditions for several parameters
are each factored into the determination of the final reaction
conditions. An important aspect of the program is that each of the
input variables can be rapidly changed, showing the resulting effect
on the other reaction parameters. This feature allows the user to
quickly experiment with different ligation reaction conditions.
Requirements: IBM PC/XT/AT/PS2 or compatible
DOS 2.1 or above
128 Kb available RAM
OR
Apple McIntosh
Program: DIGISEQ and TYPESEQ
Reference: Computer Applications in the Biosciences 3:283-286, 1987
Computer Applications in the Biosciences 4:218, 1988
Description: Two computer programs for the IBM personal computer are
described for rapid and accurate entry of DNA sequence data. The DNA
sequence files produced can be used directly by the DNA sequence
manipulation programs by R. Staden (the DataBase system), the
University of Wisconsin Genetics Computer Group, IntelliGenetics,
DNASTAR, or D. Mount. The first program, DIGISEQ, utilizes a sonic
digitizer for semi-automation of sequence entry. To enter the DNA
sequence each band of a gel reading is touched by the stylus of the
sonic digitizer. DIGISEQ corrects for both changes in lane width and
lane curvature. The algorithm is extremely efficient and rarely
requires re-entering the centers of the lanes. The second program,
TYPESEQ, uses only the keyboard for input. The keyboard is
reconfigured to place nucleotides and ambiguity codes under the
fingers of one hand, corresponding to the order of the nucleotides on
the gel defined by the user. Both programs produce individual tones
for each nucleotide, and certain ambiguity codes. This verifies input
of the correct nucleotide or ambiguity code, and thus eliminates the
need to visually check the screen display during sequence entry.
Alternatively, both programs can utilize the BigMouth voice digitizer
"speak" each nucleotide as it is entered.
Requirements: IBM PC/XT/AT/PS2 or compatible
DOS 2.1 or above
256 Kb available RAM
Program: CIP
Description: A computer program to facilitate determination of the
minimal amount of CIP to add to dephosphorylate DNA.
Requirements: IBM PC/XT/AT/PS2 or compatible
DOS 2.1 or above
128 Kb available RAM
OR
Apple McIntosh