Evalign #___________________________________________________________________________ # Title : evalign.pl # # Function : When you align any sequences by computer algorithms, you want # to know whether they are correctly aligned in terms of structures. # If the sequences are from already known structures, you can compare # and align structural sequences which can be said 'biologically correct'. # This program, 'evalign.pl' is for comparing the two sets of sequences # aligned, by calculating the absolute position differences between the # correct and computer aligned one. This is aware of gap intertions and # correct alignment made after wrong alignment segment is counted as correct. # It accepts two sequence files at prompt to calculate the differences # of positions of the sequences in the input files. The input sequences # should be identical in both files. # As an option, this also displays Percentage IDentity. # # Usage : "evalign.pl any_seq_file.msf any_struc_file.jp " while any_seq_file.msf # is a computer aligned output and any_struc_file.jp is a any seq file # from known structures. (eg, evalign.pl aa.msf aa.jp ) # # Example : evalign.pl aa.msf aa.jp -ss -H -E -p # # Argument : Two files of sequence alignment. The first one should be COMPUTER aligned # and the second one is the CORRECT (i.e., structural) alignment. # # Options : seg is for showing the accuracy of alignment on secondary str. blocks. # ss is for showing DSSP secondary structure assignment in output. # H is for showing HELIX DSSP secondary structure assignment in output. # E is for showing Beta-strand DSSP secondary structure assignment in out. # s is for sorted final output. # p is for displaying conventional percent ID. # h is for displaying help # ns is for $no_simplify by -ns, ns, Ns, NS, -Ns # seq names are sorted in final output # t= is for convert to num of 1 or 0 threshold. # c is for convert to num of 1 or 0, default threshold '1' is used # N for DO NOT Normalize the error rate which can be more than 1 digit # # $NO_normalize = 1 by N -N # $segment_rate = 1 by -seg, seg, Seg # Shows secondary str. block PSR # $show_percent_id = 1 by -p, -P, p, P, # Shows conventional percent ID. # $show_sec_str = 1 by -ss, ss or SS # Show Secondary Structure -ss option # $HELIX_only = H by -H, H # Shows conventional percent ID. # $BETA_only = E by -E, E # Shows conventional percent ID. # $print_sort = s by -s, s or S # seq names are sorted in final output # $interlaced = i by -i, i or I # seq names are sorted in final output # $no_simplify = 1 by -ns, ns, Ns, NS, -Ns # seq names are sorted in final output # $threshold = by t= # seq names are sorted in final output # $convert_to_0_or_1 = 1 by -c, C, c, Con # seq names are sorted in final output # $HELP = 1 by -h, h # for showing help # # Returns : simple shifted positions. # Author : Jong Park # Package : Part of Bioperl project. # CopyLeft : GPL # Version : 1.5 #------------------------------------------------------------------- ftp site: ftp.mrc-lmb.cam.ac.uk /pub/genomes/jong/Software/Evalign