| Function cutNs Cut out all masked sequences from a Dna5String. cutNs(sequenceCut, sequence) Include Headers seqan/alignment_free.h Parameters
sequenceCut | Dna5String similar to sequence with all Ns cut out Types: Dna5String
sequence | Masked DNA sequence. Types: Dna5String
Remarks This function concatenates the nonmasked parts of the sequence, thereby changing the word content. If you want to remove the masked parts of a sequence without concatenation, use stringToStringSet. Return Values Returns a Dna5String similar to the input sequence with all Ns cut out. Examples Transform a masked DNA sequence into an unmasked sequences with all masked parts cut out using namespace seqan; Dna5String sequenceMasked = "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG"; Dna5String sequenceMaskedPartsRemoved; cutNs(sequenceMaskedPartsRemoved, sequenceMasked); // Print the masked sequence std::cout<<sequenceMasked<<"\n"; // Print the sequence with the masked parts removed std::cout<<sequenceMaskedPartsRemoved<<"\n"; // sequenceMasked = // "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG" // sequenceMaskedPartsRemoved = // "TTTCCGAAAAGGTAGCAACTTTACGTGATCAAAGTTTTCCCCGTCGAAATTGGGTG" See Also MarkovModel, alignmentFreeComparison, stringToStringSet SeqAn - Sequence Analysis Library - www.seqan.de

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