/usr/include/ncbi/dust.h is in libncbi6-dev 6.1.20120620-10.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 | /* dust.h
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* 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 have not placed any restriction on its use or reproduction.
*
* 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.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: dust.h
*
* Author(s): Roma Tatusov, John Kuzio
*
* Version Creation Date: 5/26/95
*
* $Revision: 6.1 $
*
* File Description: a utility to find low complexity NA regions
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
* $Log: dust.h,v $
* Revision 6.1 1999/08/18 17:57:56 sicotte
* added includes for prototypes
*
* Revision 6.0 1997/08/25 18:53:06 madden
* Revision changed to 6.0
*
* Revision 5.2 1997/02/14 22:29:48 kuzio
* filter function updates
*
* Revision 5.1 1997/02/11 00:20:45 kuzio
* support for graphs added
*
* Revision 5.0 1996/05/28 13:43:15 ostell
* Set to revision 5.0
*
* Revision 4.0 1995/07/26 13:50:15 ostell
* force revision to 4.0
*
* Revision 1.1 1995/05/26 18:47:47 kuzio
* Initial revision
*
*
* ==========================================================================
*/
#include <objseq.h>
#include <seqport.h>
#include <objloc.h>
extern SeqLocPtr BioseqDust PROTO ((BioseqPtr bsp, Int4 start, Int4 end,
Int2 level, Int2 window, Int2 minwin, Int2 linker));
extern SeqLocPtr SeqLocDust PROTO ((SeqLocPtr slp,
Int2 level, Int2 window, Int2 minwin, Int2 linker));
extern FloatHiPtr DustGraph PROTO ((SeqPortPtr spp, Int4 length,
Int2 level, Int2 window, Int2 minwin, Int2 linker));
/****************************************************************************
Added notes:
the values of the BioseqDust parameters:
start, end
are passed to a SeqPortNew function, and these should be set
appropriately.
calling the functions BioseqDust or SeqLocDust with any or all of
the parameters:
window, level, minwin, linker
set to -1, sets the values for those variables to standard
dust defaults.
parameter what it is default range
level cut off score 20 2 - 64
window size of dusting window 64 8 - 256
minwin minimum length of 4 4 - 128
dusted region
linker minimum allowable 1 1 - 32
distance between
dusted regions
dust turns all totally ambiguous (N) or invalid nucleotides into
adenosines (A). the former is because dust retrieves sequence using
2-bit encoding; other ambiguities are resolved accordingly. the
latter is stubbornness on dust's part; in such cases, an
informational notice is sent out.
normalization by length isn't good. increasing the size of the
scanning window, thereby increasing the number of triplets looked
at in a pass (increasing the length), will produce different "dusts".
****************************************************************************/
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