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MKDNA6IDX(1)   MKDNA6IDX(1)

NAME

mkdna6idx - generate a six frame translation index

SYNOPSIS

mkdna6idx [options] <indexname>

DESCRIPTION

mkdna6idx is very similar to mkvtree. While mkvtree can handle sequences over arbitrary alphabets, mkdna6idx requires DNA-sequences as input. It generates two indices, namely:

•A flat index "indexname" for the the given DNA sequences. It mainly consists of the two files "indexname.tis" and "indexname.ois". This index is mainly used for output purpose.

•An index "indexname.6fr" for the given DNA sequences translated in all six reading frames.This is used for computing the matches.

Please also see the Vmatch manual for a more detailed explanation of the usage.

OPTIONS

-db <file>

Specify database files (mandatory).

-smap <file>

Specify file containing a symbol mapping. This describes the grouping of symbols. It is possible to set the environment variable MKVTREESMAPDIR to the path where these files can be found.

-transnum <table>

Perform six frame translation. Specify codon translation table by a number in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1): 



 1 Standard


 2 Vertebrate Mitochondrial


 3 Yeast Mitochondrial


 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma


 5 Invertebrate Mitochondrial


 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear


 9 Echinoderm Mitochondrial
10 Euplotid Nuclear
11 Bacterial
12 Alternative Yeast Nuclear
13 Ascidian Mitochondrial
14 Flatworm Mitochondrial
15 Blepharisma Macronuclear
16 Chlorophycean Mitochondrial
21 Trematode Mitochondrial
22 Scenedesmus Obliquus Mitochondrial
23 Thraustochytrium Mitochondrial

-indexname <string>

Specify name for index to be generated.

-cpl

Use reverse complement of the input sequence.

-tis

Output transformed input sequences (tistab) to file.

-ois

Output original input sequences (oistab) to file.

-maxdepth <len>

Restrict the sorting to prefixes of the given length.

-v

Verbose mode.

-version

Show the version of the Vmatch package

-help

Show help.

SEE ALSO

mkvtree(1)