Looking for the program Gene Jockey. Thanks!

Dan Jacobson danj at welchgate.welch.jhu.edu
Thu Apr 8 12:14:16 EST 1993


In article <47549 at sdcc12.ucsd.edu> ericg at jeeves.ucsd.edu (Eric Geerdes) writes:
>Greetings from San Diego,
>
>We're trying to find info on the program Gene Jockey.
>
>Don't know if it is public domain or not--but we do know it's
>for the Mac.
>
>Thanks for any help you might come up with.
>
>-Eric
>UCSD Biology Computer Services
>ericg at ucsd.edu
>


Gene Jockey is commercial - I'm including a little information below.
You can find a demo version of this program by gopher or anonymous ftp
from several sites - one of them being ftp.bio.indiana.edu in the molbio/mac
directory.

Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu


--------------------

 GeneJockey A program for editing, manipulating and analysing nucleic acid and protein sequences

DEMO VERSION.
	Please note that the demo version will not save or print sequences (it can,
however print this 'Read Me' window).  The global clipboard is disabled, so data
cannot be transferred into or out of the program.  The demo version can open
only GeneJockey files and Genbank files (NOT text files, DNA inspector files or
IBI Pustell files).  The communications routines are also disabled. None of
these restrictions apply to the full version.

Introduction

	GeneJockey is a program for the Apple Macintosh which makes full use of the
machine's WIMP interface.  Nucleic acid and protein sequences can be entered
from the keyboard or imported as files in other formats (Currently the program
can read or write nucleic acid files in the format of Textco's DNA Inspector and
IBI's Pustell programs.  Text files corresponding to other formats can be read,
and Genbank files in Macintosh format can be opened ).  The program displays
both sequence data and annotations in the same window, and permits multiple
windows to be open (up to 30) so that sequences can be assembled from several
sources by standard Macintosh editing techniques. Sequences entered by hand may
be verified by re-typing or by having the machine read the sequence back, using
sampled sounds rather than speech synthesis for clarity.
	Standard procedures for manipulating sequences are provided : both types of
sequence may be reversed, and nucleic acid sequences may be complemented,
inverted or translated to protein.  In each case a new window is opened to
contain the modified sequence, the original remaining unchanged.

   Basic database searching facilities are provided, and you may search your own
GeneJockey files or Genbank files or both at once.  You may search the comments
section of the files with keywords entered at the keyboard, or search the
sequence sections using the sequence currently displayed in the front window. In
either case, the program makes a crude estimate of the time required to complete
the search before starting.  Standard search facilities are provided for
searching a single sequence with a short sub-sequence, and the availability of
wild card characters allows consensus sequences to be searched for.

Sequence analysis commands include :

Align:(Simple - display the sequences in the two top windows aligned so that the
longest possible single match is obtained, or Exhaustive - stretch the sequences
where necessary to display as much homology as possible between them).  In
either case the displayed sequences remain fully editable, enabling sequence
fragments read from sequencing gels to be adjusted to obtain the best contig in
the simplest possible manner.

Matrix : Dot-plot matrix between two sequences.


Reading Frames - Display all open reading frames longer than a threshold length,
optionally starting only at a start codon and reading both strands of the
nucleic acid.  Selected areas of open reading frame can then be translated to
protein.

Hydropathicity Plot : The hydropathicity profile of protein sequences may be
displayed using either Kyte and Doolittle or Hopp and Woods methods.

Sequence Information : Displays base counts, molecular weights etc for both a
selected section of sequence and for the entire sequence.

Restriction Analysis : The program contains recognition sequences for about 400
restriction enzymes (You can change these and add more if necessary).   DNA
sequences may be analysed using a preselected list of restriction enzymes drawn
from these, and the results displayed in text form either as individual digests,
as a multiple digest, or as a graphic map. The program can automatically  select
those enzymes which can cut (or not cut) within a selected section of the
sequence.

Requirements

	The program requires a minimum of a Macintosh Plus.  In order to make use of
the Genbank sequence database a hard disk is required, and since this database
currently occupies about 30 Mbyte a large disk is necessary if you want to have
the whole of Genbank available.  If the program is to be used for extensive
database searching a faster machine is recommended to reduce waiting time.

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