Seq>Eudora>BLAST submitted

Brian Osborne bosborne at NATURE.BERKELEY.EDU
Mon Jan 16 20:46:02 EST 1995


To the Group,

A few months ago I read a request for a Macintosh utility that would
automate the submission of sequences to the NCBI BLAST server. I thought
this would be an opportunity to familiarize myself with AppleScript.
I've submitted my scripts to ftp.bio.indiana.edu site. The README is below.
Note : the package is called "Seq>Eudora>BLAST" after extraction on the
Mac, but it's called "Seq-Eudora-BLAST.sea.hqx" at ftp.bio.indiana.edu
as ">" is an illegal character in a UNIX filename.

Seq>Eudora>BLAST READ ME

Here are 2 sets of Macintosh AppleScript applications that automate your
BLAST searches. One set, the "droplets", take Drag-and-Dropped text files
containing DNA or protein sequence, extract the sequence from them, and
send them to the BLAST server at ncbi.nlm.nih.gov using the mail
application Eudora. The second set takes a DNA or protein sequence copied
to the Clipboard and sends it to the BLAST server using Eudora. The mail
messages specify BLAST parameters which are taken automatically from an
accompanying text file called "BLAST parameters".

TO USE :

Simply select the sequence files and drop the selection on top of the
desired icon, like "tblastn". Voil=E0. Or, copy a sequence to the Clipboard,
then double-click on the desired icon, like "CLIPBOARD>tblastn".

REQUIREMENTS :

*       You must have AppleScript installed.
*       You must have the file "System Folder:Extensions:Scripting
Additions:Read/Write Commands" (which is normally installed along with
AppleScript).
*       The "CLIPBOARD" applications require the enclosed Scripting
Addition "Jon's Commands", by Jon Pugh. Drag this file to the System
=46older:Extensions:Scripting Additions folder. Thanks again John.
*       You must have "Drag and Drop" capability for the "droplets" to work.
*       You must have a version of Eudora that understands Applescript,
which I believe means version 1.4 or later.
*       Also, keep the applications in the same folder as the file "BLAST
parameters". Modify "BLAST parameters" as you wish, but keep the same
format and save it as text.

DRAG AND DROP INPUT :

The "droplets" can extract the sequence from text files containing single
sequences formatted in the following ways :

*       Plain text
*       DNA Strider ASCII
*       Pearson/Fasta
*       Genbank/GB
*       EMBL
*       Zuker

CLIPBOARD INPUT :

Copy the sequence alone to the clipboard, without additional text. The
clipboard should contain only 1 sequence.

BUGS :

*       The scripts can't accept every single common sequence format.
*       The scripts can't accept multiple sequences in 1 file, or from the
Clipboard.
*       They run out of memory if the length of the sequence > 4000 characte=
rs.
*       The "CLIPBOARD" applications can only take sequence, no additional t=
ext.
*       If you're the sole user of Eudora on your Mac you'll _still_ be
prompted to open your settings file - you may want to remove the vestigial
lines using Script Editor.

If there's a problem it's possible that I can fix it. However, bear in mind
that you are using this software at your own risk, and I can not be held
responsible for troubles arising through use of these tools. Distribute or
modify this material freely. If you have suggestions for improvements I'd
certainly be interested in hearing them.

BLAST INFORMATION :

To receive the current set of instructions on using the BLAST E-mail
server, send a help message to the BLAST E-mail server address:

blast at ncbi.nlm.nih.gov

Put the word HELP on a single line in the body of the mail message. (Any
"Subject:" line will be ignored and need not be specified).


Brian Osborne
Plant Gene Expression Center
800 Buchanan St.
Albany CA USA 94710
bosborne at nature.berkeley.edu
1.15.95







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