DIVCLUS Version. 2.2. Introduction. References http://www.mrc-lmb.cam.ac.uk/genomes/divclus_home.html ftp.mrc-lmb.cam.ac.uk in the directory /pub/genomes/Geanfammer Enclosed A biological sequence handling perl subroutine library is added. (B.pl) #____________________________________________________________________________ # Title : diviclus.pl # Usage : diviclus.pl xxxxx.msp [s=100][t=30][e=30][f=2][v] # or diviclus.pl *.msp # -while xxx.msp is a file with MSP file format # # Function : 1) merges similar sequences in MSP file fomrat making # hash output. # 2) processes the merged msp contents to sort small things # 3) connects the sequences when there is any common # region between preliminary clusters. # 4) makes various files(xx.clu, xx.sat, xx.mrg) and # also shows in STDOUT. # # To controll the division of clusters, play with # the below parameters(if you do not specify, defaults: # t=30, s=100, e=30, f=3 # if you give them mulitiple fi,.es, it will process them # all together. # Example : diviclus.pl xxxxxx.msp s=90 t=40 e=10 # Above is for score 90, seqlet leng 40, evalue 10. # However, usually you dont need options. Just put xxx.msp # # Keywords : divide_clusters, diviclust, find_linker, subcluster # Options : _ for debugging. # # for debugging. # r for range attachment option # m for merge file format(.mrg) output # v for some info. printout, VERBOSE # S for taking shorter region overlapped # L for taking larger region overlapped # A for taking average region overlapped (default) # # $short_region= S by S -S # taking shorter region overlapped # $large_region= L by L -L # taking larger region overlapped # $average_region=A by A -A # taking average region overlapped # $verbose = v by v -v # $range = r by r -r # $merge = m by m -m # $sat_file = s by s -s # $dindom = d by d -d # $indup = i by i -i # $over_write = w by w -w # $optimize = o by o -o # $score = by s= # Ssearch score cutoff, default 100 # $factor = by f= # factor is for the merge proces # (misoverlap tolerance factor 3=33%, 2=50%) # factor works within msp chunk for one sequence # to filter a good mergable seqlets # $thresh = by t= # seqlet length cutoff, default 30 # $evalue = by e= # maximum evalue cutoff default 30 # # Author : Sarah A. Teichmann and Jong Park # Version : 2.1 #------------------------------------------------------------------------------