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