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
The full documentation for elph is maintained as a Texinfo
manual. If the info and elph programs are properly installed
at your site, the command
- info elph
should give you access to the complete manual.