00001 /***************************************************************************** 00002 * Copyright (C) 2000 Jim Kent. This source code may be freely used * 00003 * for personal, academic, and non-profit purposes. Commercial use * 00004 * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * 00005 *****************************************************************************/ 00006 /* codebias.h - stuff for managing codon bias and finding frame. */ 00007 #ifndef CODEBIAS_H 00008 #define CODEBIAS_H 00009 00010 #ifndef DNAUTIL_H 00011 #include "dnautil.h" 00012 #endif 00013 00014 00015 struct codonBias 00016 /* Tendency of codons to occur in a particular region. 00017 * Tables are in scaled log probability format. */ 00018 { 00019 int mark0[64]; 00020 int mark1[64][64]; 00021 }; 00022 00023 struct codonBias *codonLoadBias(char *fileName); 00024 /* Create scaled log codon bias tables based on .cod file. 00025 * You can freeMem it when you're done. */ 00026 00027 int codonFindFrame(DNA *dna, int dnaSize, struct codonBias *forBias); 00028 /* Assuming a stretch of DNA is an exon, find most likely frame that it's in. 00029 * Beware this routine will replace N's with T's in the input dna.*/ 00030 00031 00032 #endif /* CODEBIAS_H */ 00033
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