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DNAINDEX(1) User Manuals DNAINDEX(1)


dnaindex - index dna file for use with ANFO


dnaindex [ option ... ]


dnaindex builds an index for a dna file. Dna files must be indexed to be useable with anfo(1), it is possible to have multiple indices for the same dna file.


Print version number and exit.

Write output to file. file customarily ends in .idx. Default is genomename_wordsize.idx.

Read the genome from file. This file name is also stored in the resulting index so it can be found automatically whenever the index is used. It is therefore best if file is just a file name without path.

Add dir to the genome search path. This is useful if the genome to be indexed is not yet in the place where it will later be used.

Add text as description to the index. This is purely informative.

Set the wordsize to size. A smaller wordsize increases precision at the expense of higher computational investment. The default is 12, which with a stride of 8 yields a good compromise.

Set the stride to num. Only one out of num possible words of dna is actually indexed. A smaller stride increases precicion at the expense of a bigger index. The default is 8, which in conjunction with a wordsize of 12 yields a good compromise.

Prevents the indexing of words that occur more often than lim times. This can be used to ignore repetitive seeds and save the space to store them. A good default depends on the size of the genome being indexed, something like 500 works for the human genome with wordsize 12 and stride 8.

Produce a histogram of word frequencies. This can be used to get an indea how the frequency distribution to select an appropriate value for --limit.

Print a progress indicator during operation.


dnaindex is limited to genomes no longer than 4 gigabases due to its use of 32 bit indices. The index is quite large, so depending on parameters, a 64 bit platform is needed for genomes in the gigabase range.

If a genome contains IUPAC ambiguity codes, the affected seeds need to be expanded. If there are many ambiguity codes in a small region, that results in an unacceptably large index.


Colon separated list of directories searched for genome files.



The system wide configuration file for popt(3). dnaindex identifies itself as "dnaindex" to popt.


Per user configuration file for popt(3).


None known.


Udo Stenzel <>


anfo(1), fa2dna(1), popt(3), fasta(5)

OCTOBER 2009 Applications