NCBI C++ Toolkit Cross Reference


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File 219  2005-05-31 14:41:32
File   README 3039  2009-08-11 18:00:49
File 2179  2007-05-04 17:18:18
C++ file   dust_mask_app.cpp 11551  2017-08-23 14:26:08
C++ file   dust_mask_app.hpp 3325  2009-08-11 18:00:49
File   dustmasker.lst 782  2009-06-15 15:40:12
C++ file   main.cpp 1596  2016-02-16 16:55:37

ABSTRACT DustMasker is a program that identifies and masks out low complexity parts of a genome using a new and improved DUST algorithm. The main advantages of the new algorithm are symmetry with respect to taking reverse complements, context insensitivity, and much better performance. The new DUST algorithm is described in [1]. Please cite this paper in any publication that uses DustMasker. [1] Morgulis A, Gertz EM, Schaffer AA, Agarwala R. A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. SYNOPSIS dustmasker [-in input_file_name] [-out output_file_name] [-window window_size] [-level level] [-linker linker] [-infmt input_format] [-outfmt output_format] DESCRIPTIONS DustMasker takes its input as a FASTA formatted file containing one or more nucleotide sequences. It then identifies and masks out the low complexity parts of the input sequences. The results are reported as either a FASTA formatted file with low complexity regions appearing in lower case letters, or on several more compact formats that just least the low complexity intervals themselves. The behavior of DustMasker is configurable through command line options. OPTIONS In this section, command line options to DustMasker are explained. -in input_file_name default: "-" Name of the input file (or "-" for standard input). If this option is not provided, standard input is used. -infmt input_format default: "fasta" Input data format. Possible values are "fasta" and "blastdb". -level dust_level default: 20 10 times the score threshold used by symmetric DUST algorithm. For explanation, see [1]. -linker dust_linker default: 1 Maximum difference between the start of a masked interval and the end of the previous masked interval at which those intervals should be merged into one. -outfmt output_format default: interval Possible values: interval, acclist, fasta. Specifies the output format. Output format 'interval'. For each input sequence the output contains the defline (as it appears in the input file) followed by the masked subinterval of the sequence, one subinterval per line, in the form "begin - end". Output format 'acclist'. Masked intervals are reported one per line in the form: 'sequence_id begin end'. Output format 'fasta'. Output file is in the FASTA format. The content is identical to the input file except that the masked parts are written in lower case letters. -out output_file_name default: "-" Name of the output file ( or "-" for standard output ). If this option is not provided, standard output is used. -window dust_window default: 64 The length of the window used by symmetric DUST algorithm. For explanation see [1].

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