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gt-seqmutate - Online in the Cloud

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This is the command gt-seqmutate that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gt-seqmutate - Mutate the sequences of the given sequence file(s).

SYNOPSIS


gt seqmutate [option ...] [sequence_file ...]

DESCRIPTION


-rate [value]
set the mutation rate (default: 1)

-width [value]
set output width for FASTA sequence printing (0 disables formatting) (default: 0)

-o [filename]
redirect output to specified file (default: undefined)

-gzip [yes|no]
write gzip compressed output file (default: no)

-bzip2 [yes|no]
write bzip2 compressed output file (default: no)

-force [yes|no]
force writing to output file (default: no)

-help
display help and exit

-version
display version information and exit

For each position in the given sequences it is randomly determined with probability
(mutation rate / 100) if the given position is mutated. If so, in 80% of the cases a
substitution is performed, in 10% an insertion, and in 10% a deletion, respectively. For
substitution and insertion events, the nucleotide is generated randomly without regard to
the original nucleotide. That is, resubstitutions are possible. This procedure equals the
one described on page 1867 of the following paper:

T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST
sequences. Bioinformatics, 21(9):1859-1875, 2005.

REPORTING BUGS


Report bugs to <[email protected]>.

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