Mac users : automate email blast searches

Brian Osborne bosborne at NATURE.BERKELEY.EDU
Mon Feb 13 21:31:58 EST 1995


To the group,

I've written some AppleScripts to aid your email blast searches.
They're particularly useful if you send many sequences. With
these scripts you can simply drag-and-drop many text files
onto the script's icon, and the script and Eudora will do the rest.
The package is available from ftp:///ftp.bio.indiana.edu/molbio/mac.
A portion of the README :

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.



Brian I. Osborne
Plant Gene Expression Center
800 Buchanan St.
Albany CA 94710 USA
bosborne at nature.berkeley.edu
=46AX 510 559 5718
TEL 510 559 5919





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