1 #ifndef ALGO_SEQ__CONSENSUS_SPLICE__HPP
2 #define ALGO_SEQ__CONSENSUS_SPLICE__HPP
3
4 /* $Id: consensus_splice.hpp 405345 2013-07-02 18:56:07Z astashya $
5 * ===========================================================================
6 *
7 * PUBLIC DOMAIN NOTICE
8 * National Center for Biotechnology Information
9 *
10 * This software/database is a "United States Government Work" under the
11 * terms of the United States Copyright Act. It was written as part of
12 * the author's official duties as a United States Government employee and
13 * thus cannot be copyrighted. This software/database is freely available
14 * to the public for use. The National Library of Medicine and the U.S.
15 * Government have not placed any restriction on its use or reproduction.
16 *
17 * Although all reasonable efforts have been taken to ensure the accuracy
18 * and reliability of the software and data, the NLM and the U.S.
19 * Government do not and cannot warrant the performance or results that
20 * may be obtained by using this software or data. The NLM and the U.S.
21 * Government disclaim all warranties, express or implied, including
22 * warranties of performance, merchantability or fitness for any particular
23 * purpose.
24 *
25 * Please cite the author in any work or product based on this material.
26 *
27 * ===========================================================================
28 *
29 * Authors: Josh Cherry
30 *
31 * File Description: Simple functions for determining whether a pair of
32 * dinucleotides form a consensus splice sequence
33 *
34 */
35
36 #include <corelib/ncbistd.hpp>
37
38 BEGIN_NCBI_SCOPE
39
40
41 /// Consensus splice is GY..AG or AT..AC
IsConsensusSplice(const string & splice5,const string & splice3)42 inline bool IsConsensusSplice(const string& splice5,
43 const string& splice3)
44 {
45 return (NStr::EqualNocase(splice3, "AG") &&
46 (NStr::EqualNocase(splice5, "GT") ||
47 NStr::EqualNocase(splice5, "GC"))) ||
48 (NStr::EqualNocase(splice5, "AT") &&
49 NStr::EqualNocase(splice3, "AC"));
50 }
51
52
53 /// Strict consensus splice is GT..AG
IsStrictConsensusSplice(const string & splice5,const string & splice3)54 inline bool IsStrictConsensusSplice(const string& splice5,
55 const string& splice3)
56 {
57 return NStr::EqualNocase(splice5, "GT") &&
58 NStr::EqualNocase(splice3, "AG");
59 }
60
61 /// GT-{TG,GG,AT,AA} or {GA,TT,AT,GG}-AG or AT-{AT,AA}
IsKnownNonConsensusSplice(const string & splice5,const string & splice3)62 inline bool IsKnownNonConsensusSplice(const string& splice5,
63 const string& splice3)
64 {
65 return (splice5.size() == 2 && NStr::FindNoCase("GA TT AT GG", splice5) != NPOS && NStr::EqualNocase(splice3, "AG"))
66 || (NStr::EqualNocase(splice5, "GT") && splice3.size() == 2 && NStr::FindNoCase("TG GG AT AA", splice3) != NPOS)
67 || (NStr::EqualNocase(splice5, "AT") && splice3.size() == 2 && NStr::FindNoCase("AT AA", splice3) != NPOS) ;
68 }
69
70 END_NCBI_SCOPE
71
72 #endif // ALGO_SEQ__CONSENSUS_SPLICE__HPP
73