Documentation read from 01/25/2012 11:58:32 version of /scratch/FIGdisk.server/FIG/bin/svr_assign_using_figfams.
svr_assign_using_figfams [options] <proteins.fasta >functions.tbl
Assign Using the FIGfams Server
This script takes a FASTA file of proteins from the standard input and writes the function of each to the standard output. FIGfams are used to determine the function when possible. When not possible, a message will be written to the standard error output.
A number, generally from 1 to 100, indicating how careful we should be about making the assignments. A higher number indicates greater care.
If this value is nonzero, then when a function is assigned to the sequence, it will be BLASTed against one or more FIGfams that implement the function, and the top N results will be displayed, where N is this number.
Assign to all proteins.
Emit the OTU of the hits, as the first column.
Display this command's parameters and options.
The URL for the FIGfam server, if it is to be different from the default.
The standard output is a tab-delimited file. If no BLAST output is specified, the the first column of each record is a feature ID from the FASTA input, and the second column is the assigned function. If BLAST output is specified, then the BLAST hits found will be listed after each assignment. The columns in a BLAST hit record are as follows.
ID of the feature hit by the BLAST.
Percentage identity of the matching sequences.
Position in the query sequence at which the match starts.
Position in the query sequence at which the match stops.
Position in the hit sequence at which the match starts.
Position in the hit sequence at which the match stops.
P-score of the match.
Bit-score of the match.
Total length of the query sequence.
Total length of the hit sequence.
ID of the FIGfam containing the hit sequence.