HattCI is C-implementation for identification of attC sites in DNA sequences.
HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models
Pereira, Mariana Buongermino; Wallroth, Mikael; Kristiansson, Erik; and Axelson-Fisk; Marina. Journal of Computational Biology. November 2016, 23(11): 891-902. doi:10.1089/cmb.2016.0024.
HattCI is freely distributed under the GNU General Public License (GPLv3).
- Download HattCI, move it to a yourDirectory where you want it installed. Uncompress it.
- Enter Terminal.
- cd yourDirectory
- Type 'make' in terminal.
Make sure yourDirectory is in your $PATH.
To run HattCI, type
$ hattci.out <fasta file> <location to put the output file>
or
$ hattci.out the.fasta ./output/output.txt
Note that if output.txt already exists, it is overwritten.
Otherwise, it is created. If no output file is given, the output is written to
a standard file.
-b:
Processes both the ordinary sequences and the complementary
sequence.
To run for both directions, type:
$ hattci.out -b <fasta file> <location to put the output file>
-s x:
HattCI reads x sequences at a time and processes them before reading the next x sequences, in order to avoid overextending RAM. Default is 1000 sequences.
This flag gives the option to manually choose number of sequences to read, in the case of large sequences.
To specify the chunk size when reading sequences, type for instance:
$ hattci.out -s 100000 <fasta file> <location to put the output file>
-t x:
HattCI may run a large part of the computations in parallel, i.e. let different threads process a set of sequences, which in turn gives a reduced computation time. The parallelization works best when processing larger chunks of sequences at a time. Default number of threads are 1.
To specify the number of threads, type for instance:
$ hattci.out -t 4 <fasta file> <location to put the output file>
The flags works together, type for instance:
$ hattci.out -b -s 100
A tutorial with two usage examples can be find here.
- Open a Terminal
- cd the directory where it is installed
- make clean
- delete the directory