elph1

Overview

Motif finder program ELPH (Estimated Locations of Pattern Hits) Usage:

elph <multi-fasta_file> [options] OR elph <multi-fasta_file-1> <multi-fasta_file-2> [-t <matrix>] Options: -h : print this help -b : just brief results; don't print motif -d : find significance deterministically -v : find motif deterministically -o <out_file> : write output in <out_file> instead of stdout -m <motif> : use the given pattern <motif> to compute its best fit matrix

to the data

-a

: use aac residues; default = nucleotides residues

-s <seed>

: sets the seed for the random generation

-p n

: n = no of iterations before deciding local maximum; plateau

period variable

-x

: print maximum positions within sequences

-g

: find significance of motif

-t <matrix>

: test if there is significant difference between the two

input files for a given motif matrix; <matrix> is the file containing the motif matrix

-l

: compute Least Likely Consensus (LLC) for given motif

-r

: in conjunction with -m option: motif is not necessarily in

the closest edit distance from input motif

-e

: only when an additional file is used to test the significance

of the motif: find only the motifs that exactly match the input pattern (-m or -t options)

-n [0..5]

: degree of Markov chain used to generate the random file

used to test the significance of the motif default = 2

LEN=n

: n = length of motif

ITERNO=n

: n = no of iterations to compute the global maximum;

default = 10

MAXLOOP=n

: n = no of iterations to compute the local maximum;

default = 500

SGFNO=n

: n = no of iterations to compute significance of motif;

default = 1000