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". The BLAST-extract script included with these scripts extracts the BLAST results to TEXT files. Very useful when you have a lot of results. TO USE : Simply select the sequence files and drop the selection on top of the desired icon, like "tblastn". Voilˆ. 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). NOTE : READ/WRITE COMMANDS V. 1.1 DOES NOT WORK! USE AT LEAST 1.1.1. ¥ The "CLIPBOARD" applications require the enclosed Scripting Addition "Jon's Commands", by Jon Pugh. Drag this file to the System Folder: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. CONFIGURING FOR A SINGLE USER : On our Macs there are many users. Thus, the script asks for a specific individual's Eudora settings file. If you're the only one using these scripts on your computer then you may want to tailor these scripts so they don't bug you for your settings file each time. You can do this with Script Editor (installed along with AppleScript) by changing the eudoraPrefFile variable (called a property by AppleScript) at the top of the script : property eudoraPrefFile : "" -- put a single user's settings file here, like "Power HD:BrianÄ:Eudora Settings" 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 characters. ¥ The "CLIPBOARD" applications can only take sequence, no additional text. ¥ 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, but you may not sell them or use parts of them in scripts for sale. 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@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@nature.berkeley.edu © 2.15.95