Documentation read from 01/25/2012 11:58:32 version of /scratch/FIGdisk.server/FIG/bin/svr_assign_using_figfams.

svr_assign_using_figfams

svr_assign_using_figfams

Introduction

    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.

Command-Line Options

reliability

A number, generally from 1 to 100, indicating how careful we should be about making the assignments. A higher number indicates greater care.

blastOutput

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.

all

Assign to all proteins.

otu

Emit the OTU of the hits, as the first column.

help

Display this command's parameters and options.

url

The URL for the FIGfam server, if it is to be different from the default.

Output Format

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.

identifier

ID of the feature hit by the BLAST.

percentIdentity

Percentage identity of the matching sequences.

beginQuery

Position in the query sequence at which the match starts.

endQuery

Position in the query sequence at which the match stops.

beginHit

Position in the hit sequence at which the match starts.

endHit

Position in the hit sequence at which the match stops.

pScore

P-score of the match.

bitScore

Bit-score of the match.

queryLen

Total length of the query sequence.

hitLen

Total length of the hit sequence.

FIGfamID

ID of the FIGfam containing the hit sequence.