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XNU filter for amino acid sequences
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RobertBakaric/XnuFilt
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XnuFilt version 0.01 ======================= NAME: XNU Filter DESCRIPTION: This is a C++ implementation of XNU filtering strategy proposed by Jean Michel Claverie and David J. States (1993), created for identifying and masking repetitive segments in amino acid sequences. SYNOPSIS: #include<string> #include<XNU.hpp> string ProtSeq = "VGRGVQIGSPHHHHHHHHHHPQPATYQTSGNLGVSYSHSSCGPSYGSQNFSAPYSPYALNQEADVSGGYPQCAPAVYSGNLSSPMVQHHHHHQGYAGGAVGSPQYIHHSYGQEHQSLALATYN"; /* Make object */ /* Construction */ XNU<int> Xnu; /* OR */ XNU<int> Xnu(arg); // arg is : unordered_map<string, string> /* Functions */ string mask = Xnu.Filter(ProtSeq); //mask = VGRGVQIGSPXXXXXXXXXXXXXATYQTSGNLGVSYSHSSCGPSYGSQNFSAPYSPYALNQEADVSGGYPQCAPAVYSGNLSSPMVXXXXXXXGYAGGAVGSPQYIHHSYGQEHQSLALATYN CONSTRUCTION AND RUNTIME COMPLEXITY: - ACKNOWLEDGMENTS: Jean Michel Claverie & David J. States (1993) Computers and Chemistry 17: 191-201. AUTHOR: Robert Bakaric <rbakaric@irb.hr>, <bakaric@evolbio.mpg.de> COPYRIGHT AND LICENSE: * Copyright 2015 Robert Bakaric * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, * MA 02110-1301, USA.
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