Search-Launcher

Usage: search-launcher [options] [sequence_file(s)]

Options:
    -e email    Use 'email' address for searches that require it instead of
                prompting for something other than username@hostname.
    -h          Print this help message and quit.
    -s search   Perform the specified 'search' number (or name) instead
                of prompting for the search to be performed.
    -t type     Set the sequence 'type' to the given type instead of prompting
                whether this is 'protein' or 'dna' or 'blast'.
    -v          Print the version of this program and quit.

One or more sequence files can be specified on the command line.  If
no sequences are specified then you will asked to enter the sequence
file names (wildcards/globbing is allowed, i.e. '*.seq' will
work).  Enter one file name per line, enter blank line when all files
are selected.  Enter 'quit' or 'q' to quit at any point.

The sequence files can be in any format acceptable to the
READSEQ on this server. 

Prior to prompting for the search to be performed, a list of possible
protein or dna searches is provided.  Select a search by entering the
number at the beginning of the line, or the name which is the first
word in parentheses.  Some searches return results using email, they
are indicated by the word 'email' in parentheses.  Some programs
perform a single operation on multiple sequences (e.g.  multiple
sequence alignment programs); these programs are indicated by the word
'multi' in parentheses.

For most programs, a separate search is performed for each sequence in
each specified input file (more than one sequence per file is allowed
as long as the sequences are in a format accepted by the readseq
program; see above).  If an input file contains a single sequence, the
results are saved in a file with the name of the input file (with any
leading directory or folder names removed), the name of the search,
and the string 'html' separated by periods (i.e. file.blastp.html).
If an input file contains more than one sequence, the results of each
search are saved in a file with the name of the sequence, the name of
the search, and the string 'html' separated by periods
(i.e. locus1.blastp.html).  For multiple sequence alignments, a single
alignment is generated using all of the sequences in all of the input
files and the results saved in a file with the name of the first file
(with any leading directory or folder names removed), the name of the
search, and the the string 'html' separated by periods
(i.e. file1.pima.html).

The files containing the results and the log file are always saved in
the current directory or folder.  On Mac's the current folder refers
to the folder where the SearchLauncher application is and not the
folder where the sequence files are.  To have the results saved in the
folder with your sequences it is best to copy or move the
SearchLauncher application to that folder.

All results are returned as HTML files and should be viewed using
Netscape, Mosaic, Lynx or another HTML viewer (e.g., using Netscape a
HTML file can be opened using the "Open File" command under the "File"
menu). 

Send comments, errors and suggestions to B.Patel@griffith.edu.au
Created: 23 March 1997
Modified: 23 March 1997