MKDNA6IDX(1)

💖 MKDNA6IDX 💖

okay so bestie, welcome to mkdna6idx(1) — that's the manual page for the mkdna6idx command, section 1, and yes the name shows up at the bottom too because that's just how man pages do 💅

✨ NAME ✨

mkdna6idx — generate a six frame translation index 🧬

🌸 SYNOPSIS 🌸

mkdna6idx [options] <indexname>

🦋 DESCRIPTION 🦋

okay so mkdna6idx is very similar to mkvtree. like, they're cousins fr. the difference? mkvtree can handle sequences over arbitrary alphabets — it's flexible like that — but mkdna6idx requires DNA-sequences as input. no DNA, no index, periodt.

and it doesn't just make one index, it makes two:

• A flat index called indexname for the given DNA sequences. it's mainly made up of the two files indexname.tis and indexname.ois. this one is mainly used for output purpose.
• An index called indexname.6fr for the given DNA sequences translated in all six reading frames. this is the one used for computing the matches. 👑

also, please also see the Vmatch manual for a more detailed explanation of the usage — iykyk.

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🎀 OPTIONS 🎀

• -db <file> — specify database files. this one is mandatory, bestie, you literally cannot skip it 🙈
• -smap <file> — specify a file containing a symbol mapping. this describes the grouping of symbols. and get this — you can set the environment variable MKVTREESMAPDIR to the path where these files can be found. cute right? ✨
• -transnum <table> — perform six frame translation. specify the codon translation table by a number in the range [1,23], except for 7, 8, 17, 18, 19 and 20 (those ones are just not invited to the party 💀). 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 the index to be generated. name your baby 🫶
• -cpl — use the reverse complement of the input sequence. iconic behaviour honestly
• -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. she talks a lot 💬
• -version — show the version of the Vmatch package.
• -help — show help. we love a helpful queen 🌈

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🌟 SEE ALSO 🌟

mkvtree(1)

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and that's the whole page bestie!! 🎀 this was MKDNA6IDX(1) from the Vmatch package, manual section 1, and the name appears down at the bottom too like a lil signature — mwah, go index something, love u 💜✨