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Helix-turn-helix motif prediction ANSI C source
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From [email protected] Sat Apr 24 16:13:56 1993 Received: from net.bio.net by sunflower.bio.indiana.edu (4.1/9.7jsm) id AA05660; Sat, 24 Apr 93 16:13:50 EST Received: from ncar.ucar.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA05950; Sat, 24 Apr 93 14:12:05 -0700 Received: from midway.uchicago.edu by ncar.ucar.EDU (5.65/ NCAR Central Post Office 03/11/93) id AA02685; Sat, 24 Apr 93 15:12:34 MDT Received: from wakinyan.uchicago.edu by midway.uchicago.edu Sat, 24 Apr 93 16:12:32 CDT Return-Path: <[email protected]> Received: by wakinyan.uchicago.edu (4.1/UofC3.2) id AA09798; Sat, 24 Apr 93 16:13:06 CDT Newsgroups: bionet.software.sources Path: kimbark!chh9 From: [email protected] (Conrad Halling) Subject: Helix-turn-helix motif prediction ANSI C source Message-Id: <[email protected]> Sender: [email protected] (News System) Reply-To: [email protected] Organization: University of Chicago Computing Organizations Date: Sat, 24 Apr 1993 21:13:02 GMT Apparently-To: [email protected] Status: R /* hth.c v 1.0.1 24 April 1993 This simple program predicts whether a protein contains a helix-turn- helix motif, using the method of: Dodd, I. B., and J. B. Egan. 1990. Improved detection of helix-turn- helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18:5019-5026. This code written and donated to the public domain by: Conrad Halling Department of Molecular Genetics and Cell Biology University of Chicago 920 E 58th St Chicago IL 60637 e-mail: [email protected] How to compile this program: This program is written in ANSI C using THINK C 5.0.4. On our local UNIX system (running SunOS Release 4.1.1), it will not compile using cc but will compile using either gcc or acc. For example, to compile this program, you would type acc -o hth hth.c <return> This means, "start the acc (ANSI C Compiler) program, send the output to a file called "hth", and take the input from the file "hth.c". When the program is compiled, you run it by typing "hth" at the prompt. tabs = 4 When using vi under UNIX, you can set the tabs to 4 by opening the file, typing escape (to go into command mode), colon (":") to go to the command line, and "set tabstop=4" (without the quotes). Format of input protein sequence: One protein sequence per file Single-letter code in upper case and/or lower case White space characters (space, tab, return, etc.) are ignored The program will abort if an invalid character is found */ #include <ctype.h> #include <limits.h> #include <stdlib.h> #include <stdio.h> #include <string.h> #ifndef __HTH__ #define __HTH__ #ifndef TRUE #define TRUE 1 #endif #ifndef FALSE #define FALSE 0 #endif #define AMINO_ACIDS_COUNT 20 #define MAX_SEQUENCE_LENGTH 20000 #define WINDOW_SIZE 22 /* These values from Table 3 */ #define NON_HTH_MEAN_SCORE 238.71 /* of Dodd and Egan (1991) */ #define NON_HTH_STD_DEV 293.61 /* Errors */ #define NO_ERROR 0 #define SEQUENCE_TOO_SHORT 1 #define OUT_OF_MEMORY 2 #define QUIT 3 #define INVALID_CHAR 4 /* Function prototypes */ void DisplayError( short error ); void DisplayResults( double convertedScore, size_t maxScorePosition, const char *sequence ); short GetAminoAcid( char residue ); #endif const short weightMatrix[ AMINO_ACIDS_COUNT ][ WINDOW_SIZE ] = { /* A (alanine) */ -125, -194, -84, 70, 36, 54, 238, -15, 77, 26, -194, -194, -56, -84, 14, 77, -56, -56, -56, 46, -195, 36, /* C (cysteine) */ -64, -64, -63, -63, -64, -64, -64, -64, -64, 47, 47, -63, -63, -64, -64, -64, -64, -64, -64, -63, -64, 47, /* D (aspartate) */ -156, -154, -156, -154, 109, -156, -156, 109, -154, -156, 6, -156, -154, -85, -156, -156, -156, -156, -154, -154, -156, -85, /* E (glutamate) */ -31, -9, -171, 70, 156, -171, -171, 107, 50, -60, -60, -171, -60, 78, 86, -171, -171, -101, -171, -170, 86, 9, /* F (phenylalanine) */ 10, -130, 10, -130, -130, 10, -130, -129, -130, 102, -130, -130, -130, -130, -129, -130, -130, -129, -129, -129, 180, -130, /* G (glycine) */ 30, 5, -190, -51, -191, -191, 18, -191, -191, -191, 202, -191, -10, -191, 5, -190, -191, -80, -190, -190, -191, -51, /* H (histidine ) */ 62, 33, -76, -76, -7, -78, -78, 33, -7, -78, 84, -78, 33, 33, -78, -7, -78, -7, 62, 84, -78, -7, /* I (isoleucine ) */ 75, -156, 101, -45, -86, 116, -156, -16, 65, -16, -156, 128, -156, -86, -156, -155, 188, -155, -16, 53, 122, -155, /* K (lysine ) */ -31, -31, 10, 70, 79, -170, -170, 94, 70, -171, -9, -100, -100, 25, -100, -170, -171, -9, 38, -31, -9, 101, /* L (leucine) */ 66, -212, 72, -213, -212, 144, -213, -102, 37, 132, -213, 97, -213, -142, -212, -212, 97, -212, -212, 37, 88, -213, /* M (methionine) */ 122, -74, -3, -73, -73, -73, -74, -74, 88, 122, -73, 158, -74, -74, -3, -74, -3, -74, -74, -3, -74, -73, /* N (asparagine) */ -137, 72, -137, -136, -137, -137, -137, -67, -136, -136, 128, -137, 72, -136, 2, -67, -137, 2, 84, -137, -137, 104, /* P (proline) */ -156, 23, -157, -156, -157, -157, -157, -157, -157, -157, -157, -157, -46, 101, 39, -157, -157, -157, -157, -157, -157, -46, /* Q (glutamine) */ -60, -130, 175, 90, 110, -131, -131, 90, 78, -131, -131, -60, -130, 154, 65, 119, -131, -20, 119, 31, -20, 90, /* R (arginine) */ 65, 76, 110, 65, 7, -155, -154, 123, 76, -155, -154, -155, -154, 129, 54, 40, -155, 129, 179, -45, -155, 123, /* S (serine) */ -118, 96, -188, 21, -48, -187, -8, -187, -118, -118, -77, -188, 174, -187, 135, -26, -188, 150, -77, -188, -187, -26, /* T (threonine) */ 11, 149, -59, 80, -169, -8, -170, -99, -99, -30, -170, -8, 131, -30, -59, 198, -170, -30, -169, -170, -30, -59, /* V (valine) */ 17, -67, -177, -177, -108, 100, -178, -178, -108, 71, -178, 160, -178, -16, -67, -67, 169, -178, 17, 31, 17, -178, /* W (tryptophan) */ 44, -26, -26, -26, -26, -26, -26, -26, -26, -26, -26, -26, -26, -25, -26, -25, -26, -26, 44, 279, -26, -26, /* Y (tyrosine) */ -40, -110, 30, 1, -110, -109, -110, -110, -40, 30, -110, -109, -109, -40, -110, -40, -110, 162, 52, 86, -110, -110 }; const char aminoAcidsString[] = "ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy"; int main() { char fileName[ FILENAME_MAX ], format[ 12 ], residue, *sequence; int resultsDisplayed, theChar; short aminoAcid, fileNameEntered, maxScore, quit, status, tempScore; size_t i, j, length, maxWindowPosition, maxScorePosition, sequenceLength; double convertedScore; FILE *sequenceFile; status = NO_ERROR; quit = FALSE; printf( "Welcome to hth, a program that predicts whether a protein contains\n" ); printf( "a helix-turn-helix motif.\n\n" ); printf( "For more information, please read\n\n" ); printf( " Dodd, I. B., and J. B. Egan. 1990. Improved detection of\n" ); printf( " helix-turn-helix DNA-binding motifs in protein sequences.\n" ); printf( " Nucleic Acids Res. 18:5019-5026.\n\n" ); printf( "Please be sure that your protein sequence is in \"plain\" format\n" ); printf( "using the single-letter code.\n\n" ); while ( !quit ) { /* Allocate memory for the protein sequence. */ sequence = ( char * ) malloc( MAX_SEQUENCE_LENGTH * sizeof( char ) ); if ( NULL == sequence ) status = OUT_OF_MEMORY; /* Get the name of the sequence file. */ fileNameEntered = FALSE; while ( !fileNameEntered ) { printf( "Name of protein file (q/Q = Quit): " ); sprintf( format, "%%%us", FILENAME_MAX ); scanf( format, fileName ); length = strlen( fileName ); if ( 0 != length ) { /* Check for quit command. */ if ( ( 1 == length ) && ( ( fileName[ 0 ] == 'q' ) || ( fileName[ 0 ] == 'Q' ) ) ) { status = QUIT; quit = TRUE; break; } else { /* Open the sequence file. */ sequenceFile = fopen( fileName, "r" ); if ( NULL == sequenceFile ) printf( "File not found!\n\n" ); else fileNameEntered = TRUE; } } } if ( NO_ERROR == status ) { /* Read the sequence from sequenceFile into sequence[]. */ i = 0; while ( i < MAX_SEQUENCE_LENGTH ) { /* Stop reading at end of file. */ theChar = getc( sequenceFile ); if ( feof( sequenceFile ) ) break; /* Skip white space characters. */ if ( isspace( theChar ) ) continue; /* GetAminoAcid will return AMINO_ACIDS_COUNT if the character is not found in AminoAcidsString[]. */ if ( AMINO_ACIDS_COUNT == GetAminoAcid( ( char ) theChar ) ) { status = INVALID_CHAR; break; } /* The character is valid; add it to the string. */ sequence[ i++ ] = ( char ) theChar; } if ( NO_ERROR == status ) sequence[ i++ ] = 0x00; fclose( sequenceFile ); } if ( NO_ERROR == status ) { sequenceLength = strlen( sequence ); if ( sequenceLength < WINDOW_SIZE ) status = SEQUENCE_TOO_SHORT; } if ( NO_ERROR == status ) { /* Calculate the highest score for the sequence. */ maxScore = SHRT_MIN; /* defined in <limits.h> */ maxScorePosition = 0; maxWindowPosition = sequenceLength - WINDOW_SIZE; for ( i = 0; i < maxWindowPosition; i++ ) { tempScore = 0; for ( j = 0; j < WINDOW_SIZE; j++ ) { residue = sequence[ i + j ]; aminoAcid = GetAminoAcid( residue ); tempScore += weightMatrix[ aminoAcid ] [ j ]; } if ( tempScore > maxScore ) { maxScore = tempScore; maxScorePosition = i; convertedScore = ( ( double ) maxScore - NON_HTH_MEAN_SCORE ) / ( NON_HTH_STD_DEV ); if ( convertedScore >= 2.5 ) { DisplayResults( convertedScore, maxScorePosition, sequence ); resultsDisplayed = TRUE; maxScore = SHRT_MIN; } } } if ( !resultsDisplayed ) DisplayResults( convertedScore, maxScorePosition, sequence ); } DisplayError( status ); } } void DisplayResults( double convertedScore, size_t maxScorePosition, const char *sequence ) { char maxScoreString[ WINDOW_SIZE ]; short i, percentage; printf( "The score is %0.2f at position %ld.\n", convertedScore, maxScorePosition + 1 ); for ( i = 0; i < WINDOW_SIZE; i++ ) maxScoreString[ i ] = sequence[ maxScorePosition + i ]; maxScoreString[ i ] = 0x00; printf( "The sequence at this position is %s.\n", maxScoreString ); if ( convertedScore >= 4.5 ) percentage = 100; else if ( convertedScore >= 4.0 ) percentage = 90; else if ( convertedScore >= 3.5 ) percentage = 71; else if ( convertedScore >= 3.0 ) percentage = 50; else if ( convertedScore >= 2.5 ) percentage = 25; if ( convertedScore < 2.5 ) printf( "This score is not significant.\n" ); else { printf( "This score suggests an approximately %d%% probability that ", percentage ); printf( "this protein\ncontains a helix-turn-helix motif.\n\n" ); } } short GetAminoAcid( char residue ) { short i, limit; limit = strlen( aminoAcidsString ); for ( i = 0; i < limit; i++ ) { if ( residue == aminoAcidsString[ i ] ) break; } if ( i >= AMINO_ACIDS_COUNT ) i -= AMINO_ACIDS_COUNT; return ( i ); } void DisplayError( short error ) { char errorString[5][80] = { "\n\n", "The protein sequence is too short to analyze.\n\n", "There is insufficient memory to continue.\n\n", "Good-bye!\n\n", "There is an invalid character in the protein sequence.\n\n" }; printf( errorString[ error ] ); } -- Conrad Halling [email protected]