User manual
Download and extracting
You can download the Nhunt program here.Portable/static build is the cross-distro build for x86 (32bit) or amd64 (64bit) Linux systems. You can also download a source code and compile program yourself. Instructions are in README.TXT file inside the tarball.
Command for extracting files (Linux):
tar -xvf nhunt_x86.tar
File formats
Query and database files should contain sequences in FASTA format (wikipedia description).Query file should contain only one sequence (if not, the first sequence from the file will be considered as query). Database file may contain any number of sequences.
Format of an output file has three variants. Look for the '-m' parameter below.
Run the program
To run the program, type./nhunt -i inputFileName -d databaseFileName
in command line. 'inputFileName' is name of the file with query sequence, 'databaseFileName' is name of the file with database sequence(s). Default name of the output file is 'nhunt.out'.
If you run the program without any parameters,
./nhunt
you will see help message with the list of available parameters.
User parameters
Any parameter consists of key and value and is called as '-key value', where 'key' is one character and 'value' is any number of characters.List of available parameters:
- -i Query file
Name of the file with query sequence.
No default value. - -d Database file
Name of the file with database sequence(s).
No default value. - -o Output file
Nhunt report output file.
Default value: 'nhunt.out' - -e E-value threshold
Threshold for found alignments: only alignments with e-value less than this value will be shown in output file.
Real positive number.
Default value: 1.0 - -m Alignment view
Alignment view option, the format of the output file:
0 = pairwise (alignment included),
8 = tabular (no alignments itself),
9 = tabular with comment lines (no alignments itself)
Default value: 0 - -p Diagonal threshold
Z-value, threshold for diagonal selection. The less this parameter is, the program is more sensitive and slow.
Real positive number.
Default value: 10 - -w Words similarity
Two words are similar, if at least w letters coincides. The length of each word is specified as w + 1.
Integer positive number.
Default value: 5 - -r Match reward
Reward for a nucleotide match (initial reward in case of adjustment mode).
Integer positive number.
Default value: 5 - -q Penalty mismatch
Penalty for a nucleotide mismatch (initial penalty in case of adjustment mode).
Integer negative number.
Default value: -4 - -G Gap open
Cost to open a gap.
Integer positive number.
Default value: 10 - -E Gap extend
Cost to extend a gap.
Integer positive number.
Default value: 5 - -a Adjustment
Adjustment options:
0 = no adjustment,
1 = global adjustment only
2 = local adjustment only
3 = global and local adjustment
Default value: 3 - -S Strand
Query strands to search against database. 3 is both, 1 is top, 2 is bottom.
Default value: 3 - -W Alignment width
Width of output alignment rows.
Integer positive number.
Default value: 60