DotcodeR: Structural similarity search by DOT plot enCODEr for RNAs in genomic sequences
========================================================================================

Requirements
------------
* [ViennaRNA package] (http://www.tbi.univie.ac.at/RNA/) (>= 2.0)

Install
-------
$ ./configure --with-vienna-rna=/path/to/vienna-rna

Then,

$ make
$ make install

Usage
-----
$ dotcoder [OPTION]... [FILE]...

[FILE]
 At most two (gzipped) FASTA files are needed.

[OPTION]
 -d, --dna             Read DNA sequences for input
                        (default: off, i.e. RNA sequence))
 -z, --gzip            Allow gzipped files for input
                        (default: off)
 -e, --entire          Compare between two entire sequences of at most 300nt length
                        (default: off)
                        (Specifying "-e" implies "-s 0" option)

 -w, --winsize <INT>   Sliding window size in the genomic sequences
                        (default <INT> = 120)
 -s, --step <INT>      Step size of the sliding window
                        (default <INT> = 30)
                        (Specifying "-s 0" implies "-e" option)
 -c, --cutoff <INT>    Report only similarity scores >= cutoff
                        (default <INT> = 20)

 -v, --verbose         Show details
                        (default: off)
 -h, --help            Show standard help
 -H, --full-help       Show this message

References
----------
Kato, Y., Gorodkin, J. and Havgaard, J.H.
Genomic screen for structured RNAs using coarse-grained secondary structure dot plots.
submitted.
