#_____________________________________________________________________ # Title : self_self_search.pl # Usage : self_self_search.pl [o c s m r] # Function : self_to_self input database search. This matches all the # sequences to others in the given database(sequence) # Default search program is 'fasta'. You can specify it # to ssearch by using 'a=ssearch' prompt option. # It will produce 2 char size subdirectories. In them, you will # get search results stored in MSP (matching sequence pair) # file format. # Example : self_self_search.pl PDB_db.fa # Keywords : self_to_self_db_search, self self search, database search # Options : # DB= for target DB "DB=MY_FASTA.fa" # File= to get file base(root) name. "File=TARGET_DB.fa" # m for MSP format directly from FASTA or Ssearch result than through sso_to_msp to save mem # s for the big single output (msp file output I mean) # o for overwrite existing xxxx.fa files for search # c for create SSO file (sequence search out file) # r for reversing the protein sequence !! # R for attaching ranges of sequences # k= for k-tuple value. default is 1 (ori. FASTA prog. default is 2) # u= for $upper_expect_limit ## The higher the slower # l= for $lower_expect_limit # a= for choosing either fasta or ssearch algorithm # d= for defining the size of subdir made. 2 means it creates # eg, DE while 1 makes D # d for $make_gz_in_sub_dir_opt, putting resultant sso files in gz format and in single char subdir # D for $make_msp_in_sub_dir_opt, convert sso to msp and put in sub dir like /D/, /S/ # n for new format (msp2 format) # # $over_write = o by o -o # $create_sso = c by c -c # $single_big_msp = s by s -s # $msp_directly_opt = m by m -m # $reverse_query =r by r -r # $upper_expect_limit = by u= # $machine_readable = M by M -M # $do_in_batch = b by b -b # $make_msp_in_sub_dir_opt = D by D -D # $make_gz_in_sub_dir_opt = d by d -d # $new_format=n by n -n # $sub_dir_size= by d= # $add_range=R by R -R # # Returns : # Argument : # Version : 1.3 #----------------------------------------------------------------------------------- ftp site: ftp.mrc-lmb.cam.ac.uk /pub/genomes/Software/Self_self_search