/usr/include/ncbi/motif.h is in libvibrant6-dev 6.1.20120620-7.
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* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: motif.h
*
* Author: Sarah Wheelan
*
* Version Creation Date: 8/8/01
*
* $Revision: 6.1 $
*
* File Description: sequence motif search functions
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#include <ncbi.h>
#include <sequtil.h>
#include <seqport.h>
#include <actutils.h>
#include <blast.h>
#define MOT_WINSIZE 15000
#define MOT_KOZTHRESH 0.05
#define MOT_KOZLEN 9
#define MOT_SIGTHRESH 0.1
#define MOT_SIGLEN 15
#define MOT_MINPOLYASIZE 5 /* minimum #A's to call a poly(A)+ tail */
#define MOT_MAXPOLYASIZE 200 /* maximum number of nucleotides to bother */
/* scanning for a tail */
#define MOT_LINKERSIZE 8 /* maximum number of non-A's to allow on end of tail */
typedef struct motif_info {
Int4 start;
Int4 stop;
FloatHi score;
Uint1 strand;
struct motif_info PNTR next;
} MotifInfo, PNTR MotifInfoPtr;
NLM_EXTERN MotifInfoPtr MOT_MotifSearch(CharPtr motif, BioseqPtr bsp, Boolean is_prot);
NLM_EXTERN MotifInfoPtr MOT_FindRepeats(BioseqPtr bsp);
NLM_EXTERN MotifInfoPtr MOT_FindKozak(BioseqPtr bsp);
NLM_EXTERN MotifInfoPtr MOT_FindSignalPeptide(BioseqPtr bsp);
NLM_EXTERN MotifInfoPtr MOT_FindPolyA(BioseqPtr bsp);
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