svr_motif

    svr_motif [options] < ali.fa > motifs

This script identifies the conserved regions from a set of aligned sequences.

Introduction

usage: svr_motif [options] < ali.fa > motifs.tbl

       -c  coord_file   - file containing coordinates for motifs to be extracted: [beg end]
       -f  max_f_diff   - maximum fraction exceptions to consensus
       -w1 win_min      - minimum window size (D = 4)
       -w2 win_max      - maximum window size (D = 10)
       -th threshold    - threshold for average site convervation score (D = 0.6)

Command-Line options

-c coord_file

The file that contains lines of coordinates for motifs to be extracted: [beg end]

-f max_f_diff

Maximum fraction exceptions to consensus.

-w1 win_min

Minimum window size (D = 4)

-w2 win_max

Maximum window size (D = 10)

-th threshold

Threshold for average site convervation score (D = 0.6)

Input

The input set of aligned sequences is read from STDIN.

Output

The output is tab-delmited 7-column table:

  [ motif_beg motif_end avg_conserve_score consensus_seq extended_beg extended_end extended_consensus ]