1024 lines
32 KiB
Fortran
1024 lines
32 KiB
Fortran
C NIP Nucleotide interpretation program
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C
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C author: Rodger Staden, Medical Research Council Centre,
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C Laboratory of Molecular Biology, Hills Road,
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C Cambridge, England
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C 12-1-90 Closed idev if.ne.kbout after rdseq
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C 16-3-90 Removed escape after bpause
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C 5-4-90 Changed getdev to redir and removed all close(unit=idev)
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C etc (see redir)
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C 6-7-90 Added showfi
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C 9-7-90 Renamed amenu to menu
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C 14-8-90 Modified 6 phase translation
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C 22-8-90 Modified 6 phase translation so it will do all listings
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C 24-9-90 Fixed bug in graphics output for pattern search
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C 5-11-90 Very many changes for addition of file of file names
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C search for patterns - affects patternn,patternnc,nipl,
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C nip,anals89,asubs89 (rdwmt)
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C 11-12-90 Chabges relating to new way of handling pir libs. New filnll
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C here and new parameter
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C 11-1-91 Modified positional base preferences to allow standard to be
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C read form a file: call from main has extra arguments
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C 22-2-91 For find open frames and trandk send maxseq instead of idim3
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C in odrer to give sufficient space for 6 phase translation
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C 17-4-91 New splice junction search
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C 7-5-91 Many changes to do with use of feature tables
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C including the argument lists to: codons, codtdk, trandk, opentr, pltmap,
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C codimp. Also forced out use of option 38 by caling 39 instead
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C 7-6-91 New sequence library routines for cdrom format. PIR stuff junked
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C 18-7-91 trndom did not write title!
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C 18-7-91 Added titles to pattern files
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C 25-2-92 Changed call to rdseq !!!!!!!!
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C 8-5-92 upped maxseq to 330000
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C 17-6-92 Declared SIGNAL as an external as there's an intrinsic with
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C the same name under AIX
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SUBROUTINE FMAIN()
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INTEGER BOTOPT,TOPOPT
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PARAMETER (NAMLEN = 60)
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CHARACTER*(NAMLEN) FILE1,FILE2,FILE3,FILE4,FILE5,FILE6,FILE7
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CHARACTER*(NAMLEN) HELPF,POINTF,FILMAR,FILNAM,FILEIN
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CHARACTER*(NAMLEN) FOFNAM
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CHARACTER*(NAMLEN) LIBLF
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PARAMETER (BOTOPT=-10,TOPOPT=70,
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+ MAXSEQ=330000,
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+ MXSPAN=603,
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+ MAXWIN=MAXSEQ+MXSPAN,
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+ MAXWIR=330000,
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+ MAXD48=MAXWIR/48,
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+ MAXD2=MAXWIR/2,
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+ MAXD3=MAXWIR/3,
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+ MAXSD2=MAXSEQ/2,
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+ MAXSD3=MAXSEQ/3,
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+ MAXMEN=-8,
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+ MAXOPT=67,
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+ MAXDEV=9,
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+ MXWTLN = 120,
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+ IDM = 5,
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+ IDME = 17)
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PARAMETER (FILE1='EUKRIBS',
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+ FILE2='INTRONS',
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+ FILE3='ECPROMS',
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+ FILE4='ECRIBS',
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+ FILE5='RENZYM4',
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+ FILE6='RENZYM6',
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+ FILE7='RENZYMAL',
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+ HELPF='NIPHELP',
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+ POINTF='NIPHPNT',
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+ FILMAR='NIPMARG',
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+ LIBLF = 'SEQUENCELIBRARIES')
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PARAMETER (MAXMOT = 50, MAXWTS = 4000)
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CHARACTER*(NAMLEN) NAMSAV(MAXMOT)
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CHARACTER*8 KEYNS(MAXMOT)
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INTEGER HELPS(BOTOPT:TOPOPT),HELPE(BOTOPT:TOPOPT),DEVNOS(MAXDEV)
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REAL WORKR(MAXWIR)
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INTEGER WORKI(MAXWIR),OPT,MARGB(MAXOPT),MARGT(MAXOPT)
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PARAMETER (MAXWRD = 6)
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PARAMETER (MAXDIC = 4**MAXWRD)
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INTEGER WORDP(MAXDIC),WORDN(MAXDIC)
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PARAMETER (MAXNZ1 = MAXSEQ/10,
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+ MAXEN = 1000,
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+ MAXEN8 = MAXEN*8)
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INTEGER ENZYM1(MAXNZ1),ENZYM2(MAXNZ1),ENZYM3(MAXNZ1)
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INTEGER ENZYME(MAXEN8),ENZYM4(MAXNZ1)
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C MAT1 SIMPLE IDENTITY
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C MAT2 IUB SCORES 0-1
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C MAT3 IUB SCORES 0-36
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C MAT4 INVERTED REPEAT
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INTEGER MAT1(IDM,IDM),MAT2(IDME,IDME)
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INTEGER MAT3(IDME,IDME),MAT4(IDM,IDM)
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CHARACTER SEQ(MAXWIN),SEQW(MAXSEQ),PAA(5,5,5),PAAS(5,5,5)
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CHARACTER CHRSET(IDM)
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EQUIVALENCE (WORKR,WORKI)
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EQUIVALENCE (ENZYME,WORDN)
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C EXTERNALS
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EXTERNAL SIGNAL
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DATA CHRSET/'T','C','A','G','-'/
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DATA MAT1/
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+ 1,0,0,0,0,
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+ 0,1,0,0,0,
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+ 0,0,1,0,0,
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+ 0,0,0,1,0,
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+ 0,0,0,0,0/
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DATA MAT2/
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+1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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+0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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+0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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+0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,
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+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
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+0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,
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+1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,
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+1,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,
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+0,1,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,
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+0,1,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,
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+1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,
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+1,1,1,0,0,0,0,1,0,1,0,1,0,0,0,0,0,
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+1,1,0,1,0,0,1,0,1,0,1,0,1,0,0,0,0,
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+0,1,1,1,0,1,0,0,1,1,0,0,0,1,0,0,0,
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+1,0,1,1,0,1,0,1,0,0,1,0,0,0,1,0,0,
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+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0/
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DATA MAT3/
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+ 36, 0, 0, 0, 9, 0,18,18, 0, 0,18,12,12, 0,12, 9, 0,
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+ 0,36, 0, 0, 9, 0,18, 0,18,18, 0,12,12,12, 0, 9, 0,
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+ 0, 0,36, 0, 9,18, 0,18, 0,18, 0,12, 0,12,12, 9, 0,
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+ 0, 0, 0,36, 9,18, 0, 0,18, 0,18, 0,12,12,12, 9, 0,
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+ 9, 9, 9, 9,36,18,18,18,18,18,18,27,27,27,27,36, 0,
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+ 0, 0,18,18,18,36, 0, 9, 9, 9, 9, 6, 6,12,12,18, 0,
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+ 18,18, 0, 0,18, 0,36, 9, 9, 9, 9,12,12, 6, 6,18, 0,
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+ 18, 0,18, 0,18, 9, 9,36, 0, 9, 9,12, 6, 6,12,18, 0,
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+ 0,18, 0,18,18, 9, 9, 0,36, 9, 9, 6,12,12, 6,18, 0,
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+ 0,18,18, 0,18, 9, 9, 9, 9,36, 0,12, 6,12, 6,18, 0,
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+ 18, 0, 0,18,18, 9, 9, 9, 9, 0,36, 6,12, 6,12,18, 0,
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+ 12,12,12, 0,27, 6,12,12, 6,12, 6,36, 8, 8, 8,27, 0,
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+ 12,12, 0,12,27, 6,12, 6,12, 6,12, 8,36, 8, 8,27, 0,
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+ 0,12,12,12,27,12, 6, 6,12,12, 6, 8, 8,36, 8,27, 0,
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+ 12, 0,12,12,27,12, 6,12, 6, 6,12, 8, 8, 8,36,27, 0,
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+ 9, 9, 9, 9,36,18,18,18,18,18,18,27,27,27,27,36, 0,
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+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0/
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DATA MAT4/
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+ 0,0,2,1,0,
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+ 0,0,0,2,0,
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+ 2,0,0,0,0,
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+ 1,2,0,0,0,
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+ 0,0,0,0,0/
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DATA PAAS/'F','F','L','L','-','S','S','S','S','S',
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1'Y','Y','*','*','-','C','C','*','W','-',
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1'-','-','-','-','-','L','L','L','L','L',
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1'P','P','P','P','P','H','H','Q','Q','-',
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1'R','R','R','R','R','-','-','-','-','-','I','I','I','M','-',
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1'T','T','T','T','T',
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1'N','N','K','K','-','S','S','R','R','-','-','-','-','-','-',
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1'V','V','V','V','V','A','A','A','A','A','D','D','E','E','-',
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1'G','G','G','G','G',
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1'-','-','-','-','-','-','-','-','-','-',
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1'-','-','-','-','-','-','-','-','-','-',
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1'-','-','-','-','-','-','-','-','-','-'/
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DATA PAA/'F','F','L','L','-','S','S','S','S','S',
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1'Y','Y','*','*','-','C','C','*','W','-',
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1'-','-','-','-','-','L','L','L','L','L',
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1'P','P','P','P','P','H','H','Q','Q','-',
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1'R','R','R','R','R','-','-','-','-','-','I','I','I','M','-',
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1'T','T','T','T','T',
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1'N','N','K','K','-','S','S','R','R','-','-','-','-','-','-',
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1'V','V','V','V','V','A','A','A','A','A','D','D','E','E','-',
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1'G','G','G','G','G',
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1'-','-','-','-','-','-','-','-','-','-',
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1'-','-','-','-','-','-','-','-','-','-',
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1'-','-','-','-','-','-','-','-','-','-'/
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C Initialise help
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CALL INTHLP('nip', TOPOPT)
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C GET DEVICE NUMBERS
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CALL UNITNO(KBIN,KBOUT,DEVNOS,MAXDEV)
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CALL OPENGR(DEVNOS(3))
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IFORNO = 0
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LIBNO = 1
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IGORT = 0
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C CALL CLEARV
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WRITE(KBOUT,1000)
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1000 FORMAT(
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+' NIP (Nucleotide interpretation program) V7.0 July 1992',/,
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+' Author: Rodger Staden'/)
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C READ IN THE POINTERS TO THE HELP FILE
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CALL SETHLP(HELPS,HELPE,BOTOPT,TOPOPT,POINTF,DEVNOS(4),KBOUT)
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CALL INITGR(KBIN,KBOUT,HELPS(0),HELPE(0),HELPF,DEVNOS(4))
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IOK=0
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CALL INITLU(IDM)
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CALL SETPAR(IOK)
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IF(IOK.NE.0) GO TO 9999
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C GET SCREEN AND MARGIN SIZES
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CALL GETMRG(ISXMAX,ISYMAX,MARGL,MARGR,MARGB,MARGT,
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+MAXOPT,DEVNOS(1),FILMAR)
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IDEV=KBOUT
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MOPT=0
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IDIMT = 0
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2 CONTINUE
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IDEVLL = DEVNOS(5)
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IDEVEN = DEVNOS(6)
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IDEVAN = DEVNOS(7)
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IDEVDL = DEVNOS(8)
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IDEVLF = DEVNOS(9)
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CALL RDSEQ(
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+SEQ(2+MXSPAN/2),MAXSEQ,IDIMT,J1,J2,ISTART,IEND,IDIM1,IDIMB,
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+DEVNOS(1),FILNAM,KBIN,KBOUT,
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+HELPS(3),HELPE(3),HELPF,DEVNOS(4),IDEV,IFORNO,
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+IDEVLL,IDEVEN,IDEVAN,IDEVDL,
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+IDEVLF,LIBNO,LIBLF,WORKI,MAXWIR,IOK)
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C SAVE FILE NAME
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FILEIN=FILNAM
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IF(IOK.NE.0)GO TO 1
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CALL SHOWFI(KBOUT,FILEIN)
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C GIVE COMPOSITION AS A CHECK
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IF(IDIMB.GT.0)CALL BCOMP(SEQ(2+MXSPAN/2),IDIMB,J1,J2,ISTART,
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+KBOUT)
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C set pointers to sequence: all this stuff relates to buffering sequences
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C in disk files, which is no longer done. As it was such a pain to put in
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C and may become useful again it is being left, although newer functions
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C cannot be sure of conforming.
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********
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C MAXSEQ = THE DIMENSION OF THE RAM BUFFER SEQ
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C IDIMT = THE ACTUAL SEQUENCE LENGTH (AND THEREFORE THE NUMBER OF ELEMENTS
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C IN THE DISK BUFFER)
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C ISTART = THE SEQUENCE NUMBER OF THE CHARACTER OCCUPYING SEQ(1)
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C J1 = THE SEQUENCE NUMBER OF THE FIRST CHARACTER IN THE ACTIVE REGION
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C J2 = THE SEQUENCE NUMBER OF THE LAST CHARACTER IN THE ACTIVE REGION
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C IDIM1 = J2-J1+1 I.E. THE NUMBER OF ELEMENTS IN THE ACTIVE REGION
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C IEND = THE SEQUENCE NUMBER OF THE LAST ELEMENT OF SEQ
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C IDIMB = IEND-ISTART+1 I.E. THE NUMBER OF ELEMENTS IN THE RAM BUFFER
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********
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IDIM1P=IDIMB+MXSPAN
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C need array size divisible by 3 for translation
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IDIM3=3*((IDIMB+3)/3)
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1 CONTINUE
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CALL BPAUSE(KBIN,KBOUT,IOK)
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C IF(IOK.NE.0)GO TO 9999
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C give menu, get option
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C
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CALL MENU(OPT,KOPT,MOPT,MAXOPT,MAXMEN,KBIN,KBOUT,
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+HELPS(0),HELPE(0),HELPF,DEVNOS(4))
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C
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C change region
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C
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IF((OPT.EQ.4).AND.(IDIMT.GT.0))THEN
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C CALL REDEFA
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C + (SEQ(2+MXSPAN/2),IDIMT,J1,J2,MAXSEQ,IDIM1,ISTART,IEND,IDIMB,
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C + DEVNOS(5),KBIN,KBOUT,
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C + IOK,SEQW,LREC,NREC,
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C + HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),MACTYP,MACSHT,MACLNG)
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CALL GTREG(KBIN,KBOUT,ISTART,IEND,J1,J2,
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+ 'Define active region',
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IOK)
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IDIM1 = J2 - J1 + 1
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GO TO 1
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END IF
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C
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C STOP
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C
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IF(OPT.EQ.2)GO TO 9999
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C
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C LIST
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C
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IF((OPT.EQ.5).AND.(IDIMB.GT.0))THEN
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CALL LSTSEQ(SEQ(2+MXSPAN/2),IDIMB,IDEV,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),ISTART,IEND,IDIMT,KOPT)
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GO TO 1
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END IF
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C
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C codon usage method to find genes
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C
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IF((OPT.EQ.42).AND.(IDIM1.GT.0))THEN
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CALL PCODUS(
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+ SEQ,IDIM1P,IEND,MXSPAN,
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+ ISXMAX,ISYMAX,J1,J2,ISTART,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
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+ DEVNOS(1),FILNAM,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA)
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GO TO 1
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END IF
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C
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C fickett
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C
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IF((OPT.EQ.48).AND.(IDIM1.GT.0)) THEN
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CALL FICKET(SEQ,IDIM1P,IDIM1,MXSPAN,
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+ ISXMAX,ISYMAX,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
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+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
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GO TO 1
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END IF
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C
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C dinucfreq
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C
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IF((OPT.EQ.22).AND.(IDIM1.GT.0))THEN
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CALL DINUCF(SEQ(2+MXSPAN/2),IDIMB,
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+ J1-ISTART+1,J2-ISTART+1,IDEV,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
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GO TO 1
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END IF
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C
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C BASE COMPOSITION
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C
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IF((OPT.EQ.21).AND.(IDIM1.GT.0))THEN
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CALL BCOMP(SEQ(2+MXSPAN/2),IDIMB,
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+ J1,J2,ISTART,IDEV)
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GO TO 1
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END IF
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C
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C WRITE OUT ACTIVE SEQUENCE
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C
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IF((OPT.EQ.8).AND.(IDIM1.GT.0))THEN
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CALL WRTACT(DEVNOS(1),FILNAM,KBIN,KBOUT,
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+ SEQ(J1+1-ISTART+1+MXSPAN/2),IDIM1,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
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GO TO 1
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END IF
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C
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C ruler
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C
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IF((OPT.EQ.12).AND.(IDIM1.GT.0))THEN
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CALL RULER(J1,J2,MARGL,MARGR,
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+ MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,KBIN,KBOUT,1,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
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GO TO 1
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END IF
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C
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C composition
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C
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IF((OPT.EQ.24).AND.(IDIM1.GT.0))THEN
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CALL COMPN(SEQ,IDIM1P,MXSPAN,
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+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
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+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
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GO TO 1
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END IF
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C
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C composition chi
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C
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IF((OPT.EQ.25).AND.(IDIM1.GT.0))THEN
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CALL CCHI(SEQ,IDIM1P,MXSPAN,
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+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
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+ J1,J2,ISTART,IEND,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),WORKR,KOPT)
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GO TO 1
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END IF
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C
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C dichi
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C
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IF((OPT.EQ.26).AND.(IDIM1.GT.0))THEN
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CALL DICHI(SEQ,IDIM1P,MXSPAN,
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+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
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+ J1,J2,ISTART,IEND,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),WORKR,KOPT)
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GO TO 1
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END IF
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C
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C trichi
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C
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IF((OPT.EQ.27).AND.(IDIM1.GT.0))THEN
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CALL TRICHI(SEQ,IDIM1P,MXSPAN,
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+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
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+ J1,J2,ISTART,IEND,KBIN,KBOUT,
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+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),WORKR,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C negentropy
|
|
C
|
|
IF((OPT.EQ.59).AND.(IDIM1.GT.0))THEN
|
|
CALL NEGENT(SEQ,IDIM1P,MXSPAN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1,J2,ISTART,IEND,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),WORKR,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C ribosomes (prokaryotic)
|
|
C
|
|
IF((OPT.EQ.58).AND.(IDIM1.GT.0))THEN
|
|
CALL PRIBS(SEQ(2+MXSPAN/2),IDIMB,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ DEVNOS(1),FILE4,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C clear all
|
|
C
|
|
IF(OPT.EQ.10) THEN
|
|
CALL CLEARG
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C xhairs
|
|
C
|
|
IF((OPT.EQ.13).AND.(IDIM1.GT.0))THEN
|
|
XMAX=J2
|
|
XMIN=J1
|
|
YMAX=ISYMAX
|
|
YMIN=0.
|
|
IIIIX=0
|
|
IIIIY=0
|
|
CALL CLEARV
|
|
CALL XHAIRN(XMAX,XMIN,YMAX,YMIN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,IIIIX,IIIIY,N,KBOUT,
|
|
+ SEQ(2+MXSPAN/2),ISTART,IDIMB,
|
|
+ SEQ(2+MXSPAN/2),ISTART,IDIMB,1)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C clear vt100
|
|
C
|
|
IF(OPT.EQ.11)THEN
|
|
CALL CLEARV
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C CHANGE MARGINS
|
|
C
|
|
IF(OPT.EQ.14)THEN
|
|
CALL MARGC(ISXMAX,ISYMAX,MARGL,MARGR,MARGB,MARGT,
|
|
+ HELPS(OPT),HELPE(OPT),MAXOPT,HELPF,DEVNOS(4),KBIN,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C reverse
|
|
C
|
|
IF((OPT.EQ.29).AND.(IDIMB.GT.0))THEN
|
|
WRITE(KBOUT,4001)J1,J2
|
|
4001 FORMAT(' Reverse and complement sequence from',I7,' to',I7)
|
|
CALL SQREV(SEQ(2+(MXSPAN/2)-ISTART+J1),IDIM1)
|
|
CALL SQCOM(SEQ(2+(MXSPAN/2)-ISTART+J1),IDIM1)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C translation list
|
|
C
|
|
C IF((OPT.EQ.38).AND.(IDIMB.GT.0))THEN
|
|
C CALL TRAN3(SEQ(2+MXSPAN/2),IDIMB,SEQW,IDIM3,
|
|
C + IDEV,DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
C + HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),ISTART,IEND,IDIMT,
|
|
C + PAA)
|
|
C GO TO 1
|
|
C END IF
|
|
C
|
|
C Analyse frequencies of repeats
|
|
C
|
|
IF((OPT.EQ.38).AND.(IDIM1.GT.0))THEN
|
|
CALL SQTREE(SEQ(J1-ISTART+2+MXSPAN/2),WORKI,IDIM1,
|
|
+ WORDP,MAXDIC,WORKI(IDIM1+1),MAXWIR-IDIM1+1,
|
|
+ ENZYME,MAXEN8,IDM,ISTART,
|
|
+ IDEV,KBIN,KBOUT,HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C translation to disk
|
|
C
|
|
IF((OPT.EQ.40).AND.(IDIM1.GT.0))THEN
|
|
CALL TRANDK(SEQ(2+MXSPAN/2),IDIMB,SEQW,MAXSEQ,
|
|
+ ISTART,IEND,IDIMT,
|
|
+ DEVNOS(1),DEVNOS(8),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,J1,J2,
|
|
+ WORKI,MAXSEQ)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C longest open frame
|
|
C
|
|
IF((OPT.EQ.54).AND.(IDIM1.GT.0))THEN
|
|
CALL OPENFR(SEQ(2+MXSPAN/2),IDIMB,J1,J2,ISTART,
|
|
+ IDEV,KBIN,KBOUT,PAA,
|
|
+ SEQW,MAXSEQ,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C codons and base composition and molecular weights
|
|
C
|
|
IF((OPT.EQ.23).AND.(IDIMB.GT.0))THEN
|
|
CALL CODONS(SEQ(2+MXSPAN/2),IDIMB,J1,J2,IDEV,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,WORKI,MAXSEQ,SEQW)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C shepherd
|
|
C
|
|
IF((OPT.EQ.47).AND.(IDIM1.GT.0)) THEN
|
|
CALL SHEPED(
|
|
+ SEQ,IDIM1P,IDIM1,MXSPAN,
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,MARGL,MARGR,
|
|
+ MARGB(OPT),MARGT(OPT),KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C positional base preferences for average amino acid composition
|
|
C
|
|
IF((OPT.EQ.43).AND.(IDIM1.GT.0)) THEN
|
|
CALL PBASEP(
|
|
+ SEQ,IDIM1P,MXSPAN,
|
|
+ ISXMAX,ISYMAX,J1,J2,ISTART,IEND,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,DEVNOS(1),
|
|
+ FILNAM,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C hairpins
|
|
C
|
|
IF((OPT.EQ.30).AND.(IDIM1.GT.0))THEN
|
|
CALL HAIRPN(SEQ(2+MXSPAN/2),IDIMB,WORKI(1),
|
|
+ WORKI(1+MAXD3),
|
|
+ WORKI(1+2*MAXD3),MAXD3,MARGL,MARGR,MARGB(OPT),
|
|
+ MARGT(OPT),ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ ISTART,IDEV,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C plot map
|
|
C
|
|
IF((OPT.EQ.16).AND.(IDIM1.GT.0))THEN
|
|
CALL PLTMAQ(DEVNOS(1),FILNAM,WORKI,MAXSEQ,MARGL,MARGR,
|
|
+ MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,J1,J2,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C reading frames using codon improbability expecting codon frequencies
|
|
C to depend on base composition
|
|
C
|
|
IF((OPT.EQ.45).AND.(IDIM1.GT.0)) THEN
|
|
CALL IMPBC(
|
|
+ SEQ,IDIM1P,IDIM1,MXSPAN,WORKR,
|
|
+ IDIM1P,ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),
|
|
+ MARGT(OPT),KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C new file
|
|
C
|
|
IF(OPT.EQ.3)GO TO 2
|
|
C
|
|
C SPLICE JUNCTIONS
|
|
C
|
|
IF((OPT.EQ.62).AND.(IDIM1.GT.0)) THEN
|
|
C CALL SPLIC1(
|
|
C + SEQ(2+MXSPAN/2),IDIMB,
|
|
C + ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
C + MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
C + DEVNOS(1),
|
|
C + FILE2,KBOUT)
|
|
C GO TO 1
|
|
CALL FSPLIC(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ DEVNOS(1),FILE2,FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,
|
|
+ WORKI,WORKR(1+MXWTLN*IDM),WORKR(1+2*MXWTLN*IDM),
|
|
+ WORKI(1+3*MXWTLN*IDM),WORKI(1+3*MXWTLN*IDM+MXWTLN),
|
|
+ WORKI(1+3*MXWTLN*IDM+2*MXWTLN),
|
|
+ WORKI(1+3*MXWTLN*IDM+3*MXWTLN),
|
|
+ WORKI(1+3*MXWTLN*IDM+4*MXWTLN),
|
|
+ IDM,MXWTLN,SEQW,CHRSET,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C
|
|
C SPLICE JUNCTIONS AG,GT NOT OBLIGATORY
|
|
C
|
|
C IF((OPT.EQ.63).AND.(IDIM1.GT.0))CALL SPLIC2(
|
|
C +SEQ(2+MXSPAN/2),IDIMB,
|
|
C 1ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
C +MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
C +DEVNOS(1),FILE2,KBOUT)
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C SPLICE JUNCTIONS AG,GT REMOVED
|
|
C
|
|
C IF((OPT.EQ.64).AND.(IDIM1.GT.0))CALL SPLIC3(
|
|
C +SEQ(2+MXSPAN/2),IDIMB,
|
|
C 1ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
C +MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
C +DEVNOS(1),FILE2,KBOUT)
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C
|
|
C signal searches from named plot files
|
|
C
|
|
IF((OPT.EQ.63).AND.(IDIM1.GT.0))THEN
|
|
CALL SIGNAL(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,
|
|
+ WORKI,WORKR(1+MXWTLN*IDM),WORKI(1+2*MXWTLN*IDM),
|
|
+ IDM,MXWTLN,SEQW,CHRSET,KOPT,2)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C PLOT WORD FREQ/ EXPECTED WORD FREQ
|
|
C
|
|
IF((OPT.EQ.64).AND.(IDIM1.GT.0))THEN
|
|
CALL WORDFP(SEQ,IDIM1P,IDIMB,MXSPAN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1,J2,ISTART,IEND,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C PROKARYOTIC PROMOTERS
|
|
C
|
|
IF((OPT.EQ.55).AND.(IDIM1.GT.0)) THEN
|
|
CALL PPROM1(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ DEVNOS(1),FILE3,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C
|
|
C PROKARYOTIC PROMOTERS ON COMPLEMENTARY STRAND
|
|
C
|
|
IF((OPT.EQ.56).AND.(IDIM1.GT.0)) THEN
|
|
CALL PPROM3(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ DEVNOS(1),FILE3,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C
|
|
C PROKARYOTIC PROMOTERS -35 AND -10 SEPARATELY
|
|
C
|
|
IF((OPT.EQ.57).AND.(IDIM1.GT.0)) THEN
|
|
CALL PPROM2(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ DEVNOS(1),FILE3,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C +HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
C
|
|
C ribosomes (eukaryotic)
|
|
C
|
|
IF((OPT.EQ.61).AND.(IDIM1.GT.0)) THEN
|
|
CALL RIBEUK(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ DEVNOS(1),FILE1,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C polyA
|
|
C
|
|
IF((OPT.EQ.65).AND.(IDIM1.GT.0)) THEN
|
|
CALL SRCHP(
|
|
+ SEQ(2+MXSPAN/2),
|
|
+ IDIMB,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C type text
|
|
C
|
|
IF(OPT.EQ.6) THEN
|
|
CALL TTEXT(DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C help
|
|
C
|
|
IF(OPT.EQ.1) THEN
|
|
CALL HELP(HELPS,HELPE,BOTOPT,TOPOPT,HELPF,DEVNOS(4),
|
|
+ KBIN,KBOUT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C start codons
|
|
C
|
|
IF((OPT.EQ.50).AND.(IDIM1.GT.0))THEN
|
|
CALL CLEARV
|
|
CALL STARTS(SEQ(2+MXSPAN/2),IDIMB,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,PAA)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C stop codons
|
|
C
|
|
IF((OPT.EQ.51).AND.(IDIM1.GT.0))THEN
|
|
CALL CLEARV
|
|
CALL STOPS(SEQ(2+MXSPAN/2),IDIMB,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,PAA)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C stop codons complementary
|
|
C
|
|
IF((OPT.EQ.52).AND.(IDIM1.GT.0))THEN
|
|
CALL CLEARV
|
|
CALL STOPSC(SEQ(2+MXSPAN/2),IDIMB,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,PAA)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C stop codons complementary and normal
|
|
C
|
|
IF((OPT.EQ.53).AND.(IDIM1.GT.0))THEN
|
|
CALL CLEARV
|
|
CALL STOPSB(SEQ(2+MXSPAN/2),IDIMB,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,PAA)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C codon improbability
|
|
C
|
|
IF((OPT.EQ.28).AND.(IDIMB.GT.0))THEN
|
|
CALL CODIMP(SEQ(2+MXSPAN/2),IDIMB,WORKR,IDIMB,DEVNOS(1),
|
|
+ FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),J1,J2,IDEV,
|
|
= WORKI(101),MAXSEQ-101,SEQW)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C REPEATS
|
|
C
|
|
IF((OPT.EQ.32).AND.(IDIM1.GT.0))THEN
|
|
IF(IDIM1.LE.MAXWIR)THEN
|
|
CALL PREPT1(
|
|
+ SEQ(2+MXSPAN/2),WORKI,IDIMB,J1,J2,ISTART,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,KOPT,
|
|
+ WORDP,WORDN,MAXWRD,MAXDIC)
|
|
ELSE
|
|
WRITE(KBOUT,1001)MAXWIR
|
|
1001 FORMAT(' Maximum length of active region for this option=',
|
|
+ I7)
|
|
END IF
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C codons to disk
|
|
C
|
|
IF((OPT.EQ.41).AND.(IDIMB.GT.0)) THEN
|
|
CALL CODTDK(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,J1,J2,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,WORKI,MAXSEQ,SEQW)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C zdna
|
|
C
|
|
IF((OPT.EQ.33).AND.(IDIM1.GT.0))THEN
|
|
CALL ZDNA(SEQ,IDIM1P,MXSPAN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C zdna runs of RY or YR
|
|
C
|
|
IF((OPT.EQ.34).AND.(IDIM1.GT.0)) THEN
|
|
CALL ZDNARN(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C zdnaROD
|
|
C
|
|
IF((OPT.EQ.35).AND.(IDIM1.GT.0))THEN
|
|
CALL ZDNARD(SEQ,IDIM1P,MXSPAN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C base phasing due to coding
|
|
C
|
|
IF((OPT.EQ.44).AND.(IDIM1.GT.0)) THEN
|
|
CALL BPHASE(
|
|
+ SEQ,IDIM1P,IDIM1,MXSPAN,
|
|
+ ISXMAX,ISYMAX,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ J1-ISTART+1,J2-ISTART+1,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C trna
|
|
C
|
|
IF((OPT.EQ.49).AND.(IDIM1.GT.0)) THEN
|
|
CALL TRNA(SEQ(2+MXSPAN/2),IDIMB,J1-ISTART+1,J2-ISTART+1,
|
|
+ ISTART,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ IDEV,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C REPEATS
|
|
C
|
|
IF((OPT.EQ.31).AND.(IDIM1.GT.0))THEN
|
|
IF(IDIM1.LE.MAXWIR)THEN
|
|
CALL PREPT2(
|
|
+ SEQ(2+MXSPAN/2),WORKI,IDIMB,J1,J2,ISTART,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,KOPT,
|
|
+ WORDP,WORDN,MAXWRD,MAXDIC)
|
|
ELSE
|
|
WRITE(KBOUT,1001)MAXWIR
|
|
END IF
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C reading frame search using codon improbability expecting even codons per
|
|
C acid
|
|
C
|
|
IF((OPT.EQ.46).AND.(IDIM1.GT.0)) THEN
|
|
CALL IMPAC(
|
|
+ SEQ,IDIM1P,IDIM1,MXSPAN,WORKR,
|
|
+ IDIM1P,ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C new search
|
|
C
|
|
IF((OPT.EQ.17).AND.(IDIM1.GT.0)) THEN
|
|
KOPT = 1
|
|
CALL SEARCH(SEQ(2+MXSPAN/2),IDIMB,J1,J2,ISTART,SEQW,MAXSD3,
|
|
+ SEQW(1+MAXSD3),MAXSD3,
|
|
+ SEQW(1+2*MAXSD3),MAXSD3,
|
|
+ ENZYM1,ENZYM2,ENZYM3,ENZYM4,MAXNZ1,
|
|
+ ENZYME,ENZYME(1+MAXEN),ENZYME(1+2*MAXEN),ENZYME(1+3*MAXEN),
|
|
+ ENZYME(1+4*MAXEN),ENZYME(1+5*MAXEN),ENZYME(1+6*MAXEN),
|
|
+ ENZYME(1+7*MAXEN),MAXEN,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,IDEV,
|
|
+ DEVNOS(1),FILNAM,FILE5,FILE6,FILE7,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),PAA,WORKI,WORDP,MAXDIC,
|
|
+ KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C Translate and list 0-6 phases
|
|
C
|
|
IF((OPT.EQ.39).AND.(IDIM1.GT.0))THEN
|
|
CALL OPENTR(SEQ(2+MXSPAN/2),IDIMB,ISTART,
|
|
+ IDEV,KBIN,KBOUT,PAA,
|
|
+ SEQW,MAXSEQ,WORKI,WORKI(IDIMB+1),MAXSEQ-IDIMB,
|
|
+ DEVNOS(1),FILNAM,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C GET DISK OUTPUT FILE ON UNIT DEVNOS(2) IF REQUIRED
|
|
C
|
|
IF(OPT.EQ.7)THEN
|
|
CALL REDIR(IDEV,DEVNOS(2),DEVNOS(3),IGORT,FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C signal searches from named plot files
|
|
C
|
|
IF((OPT.EQ.20).AND.(IDIM1.GT.0))THEN
|
|
CALL SIGNAL(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,
|
|
+ WORKI,WORKR(1+MXWTLN*IDM),WORKI(1+2*MXWTLN*IDM),
|
|
+ IDM,MXWTLN,SEQW,CHRSET,KOPT,1)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C SIGNAL SEARCH ON DINUCLEOTIDES
|
|
C
|
|
IF((OPT.EQ.60).AND.(IDIM1.GT.0)) THEN
|
|
CALL DISIG(
|
|
+ SEQ(2+MXSPAN/2),IDIMB,MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1-ISTART+1,J2-ISTART+1,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),IDEV,
|
|
+ WORKI,WORKR(1+MXWTLN*IDM*IDM),WORKI(1+2*MXWTLN*IDM*IDM),
|
|
+ IDM,MXWTLN,SEQW,CHRSET,KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C SEQFIT
|
|
C
|
|
IF((OPT.EQ.18).AND.(IDIM1.GT.0))THEN
|
|
CALL SEQFIT(SEQ(2+MXSPAN/2),IDIMB,SEQW,MAXSEQ,
|
|
+ WORKI,WORKI(1+MAXD2),MAXD2,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,
|
|
+ J1,J2,ISTART,IDEV,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C SEPFIT
|
|
C
|
|
IF((OPT.EQ.19).AND.(IDIM1.GT.0))THEN
|
|
CALL SEPFIT(SEQ(2+MXSPAN/2),IDIMB,SEQW,MAXSEQ,
|
|
+ WORKI,WORKI(1+MAXD2),MAXD2,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,J1,J2,
|
|
+ ISTART,IDEV,
|
|
+ DEVNOS(1),FILNAM,KBIN,KBOUT,MAT3,IDME,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),KOPT)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C LOCAL SIMILARITY OR COMPLEMENTARITY
|
|
C
|
|
IF((OPT.EQ.36).AND.(IDIM1.GT.0))THEN
|
|
CALL LOCALF(SEQ(2+MXSPAN/2),IDIMB,SEQW,SEQW(MAXSD2+1),MAXSD2,
|
|
+ WORKI,WORKI(1+MAXD2),MAXD2,
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),
|
|
+ ISXMAX,ISYMAX,J1,J2,ISTART,
|
|
+ IDEV,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),DIALOG)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C SET GENETIC CODE
|
|
C
|
|
IF(OPT.EQ.37) THEN
|
|
CALL SETGEN(PAAS,PAA,KBIN,KBOUT,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C WRITE LABELS
|
|
C
|
|
IF(OPT.EQ.15) THEN
|
|
CALL LABLER(KBIN,KBOUT,ISXMAX,ISYMAX,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4))
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C CHANGE DNA TO RNA OR RNA TO DNA
|
|
C
|
|
IF((OPT.EQ.66).AND.(IDIM1.GT.0))THEN
|
|
WRITE(KBOUT,1002)ISTART,IEND
|
|
1002 FORMAT(' Exchange T and U for the region',I7,' TO',I7)
|
|
CALL DNARNA(SEQ(2+MXSPAN/2),IDIMB)
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C SHOW SETTINGS
|
|
C
|
|
IF(OPT.EQ.9)THEN
|
|
WRITE(KBOUT,4000)FILEIN,J1,J2,IDIM1
|
|
4000 FORMAT(' Sequence=',A,/,' Start=',I7,' End=',I7,
|
|
+' LENGTH=',I7)
|
|
C THIS NEXT LINE IS BECAUSE SOMETIMES THE FILE IS NOT READY TO EDIT!
|
|
CLOSE(UNIT=DEVNOS(2))
|
|
CALL SEQEDT(SEQ(2+MXSPAN/2),MAXSEQ,IDIMB,KBIN,
|
|
+ KBOUT,HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),DEVNOS(1),
|
|
+ FILNAM,FILEIN,IDM,IOK)
|
|
IF(IOK.NE.0) GO TO 1
|
|
********
|
|
C MAXSEQ = THE DIMENSION OF THE RAM BUFFER SEQ
|
|
C IDIMT = THE ACTUAL SEQUENCE LENGTH (AND THEREFORE THE NUMBER OF ELEMENTS
|
|
C IN THE DISK BUFFER)
|
|
C ISTART = THE SEQUENCE NUMBER OF THE CHARACTER OCCUPYING SEQ(1)
|
|
C J1 = THE SEQUENCE NUMBER OF THE FIRST CHARACTER IN THE ACTIVE REGION
|
|
C J2 = THE SEQUENCE NUMBER OF THE LAST CHARACTER IN THE ACTIVE REGION
|
|
C IDIM1 = J2-J1+1 I.E. THE NUMBER OF ELEMENTS IN THE ACTIVE REGION
|
|
C IEND = THE SEQUENCE NUMBER OF THE LAST ELEMENT OF SEQ
|
|
C IDIMB = IEND-ISTART+1 I.E. THE NUMBER OF ELEMENTS IN THE RAM BUFFER
|
|
C IDIM3 = A BUFFER SIZE USED BY TRANSLATION ROUTINE
|
|
C THIS IS A FUDGE AND ONLY WORKS FOR UNBUFFERED SEQUENCES!!!!!!!!!!!
|
|
J1 = 1
|
|
J2 = IDIMB
|
|
IDIMT = IDIMB
|
|
IEND = IDIMB
|
|
IDIM1 = IDIMB
|
|
IDIM3=3*((IDIMB+3)/3)
|
|
WRITE(KBOUT,4000)FILEIN,J1,J2,IDIM1
|
|
GO TO 1
|
|
END IF
|
|
C
|
|
C PATTERN SEARCH
|
|
C
|
|
IF((OPT.EQ.67).AND.(IDIM1.GT.0))THEN
|
|
CALL PATTEN(SEQ(J1-ISTART+2+MXSPAN/2),IDIM1,SEQW,MAXSEQ,
|
|
+ WORKI(1),WORKI(MAXMOT+1),WORKI(2*MAXMOT+1),WORKI(3*MAXMOT+1),
|
|
+ WORKI(4*MAXMOT+1),WORKI(5*MAXMOT+1),WORKI(6*MAXMOT+1),
|
|
+ WORKI(7*MAXMOT+1),WORKI(8*MAXMOT+1),WORKI(9*MAXMOT+1),
|
|
+ WORKI(10*MAXMOT+1),WORKI(11*MAXMOT+1),WORKI(12*MAXMOT+1),
|
|
+ WORKI(13*MAXMOT+1),WORKI(14*MAXMOT+1),WORKI(15*MAXMOT+1),
|
|
+ WORKI(16*MAXMOT+1),WORKI(17*MAXMOT+1),WORKI(18*MAXMOT+1),
|
|
+ WORKI(19*MAXMOT+1),WORKI(20*MAXMOT+1),
|
|
+ WORKR(22*MAXMOT+1),WORKR(23*MAXMOT+1),
|
|
+ FILNAM,MAXMOT,MAXWTS,IDEV,DEVNOS(6),DEVNOS(7),
|
|
+ MARGL,MARGR,MARGB(OPT),MARGT(OPT),ISXMAX,ISYMAX,J1,
|
|
+ KBIN,KBOUT,DEVNOS(8),IDM,SEQ(1),IDME,
|
|
+ MAT1,MAT2,MAT3,MAT4,NAMSAV,KEYNS,
|
|
+ HELPS(OPT),HELPE(OPT),HELPF,DEVNOS(4),FOFNAM,DEVNOS(1))
|
|
C NB IVE SENT THE START OF SEQ TO BE USED IN PATTEN. THIS IS OK
|
|
C AS LONG AS MAXMOT<MXSPAN/2, AND NO MOTIF REQUIRES TO START TO
|
|
C THE LEFT OF THE FIRST REAL SEQUENCE ELEMENT
|
|
GO TO 1
|
|
END IF
|
|
GO TO 1
|
|
C
|
|
9999 CONTINUE
|
|
CALL SHUTD
|
|
END
|