How-to-Use

On the Linux command prompt. Enter the command of your needs as the following description.

Usage: ./lowComplexity [-s SbjFileName] [-o OutputFileName] [OPTIONS]

SbjFileName ........: File contains FASTA-formated subject sequences.

OutputFileName .....: File for text output.

OPTIONS:

-v Threshold .......: Minimum value to accept a window.

-w WindowSize ......: Window size.

-l SegmentLength ...: Minimum Length of the found segment to be accepted.

-p OutputOption ....: Output format. [=0,1,2,3]

[=0]: Local Convergence regions only.

[=1]: Complex output for Local Convergence regions.

[=2]: Mask Local Convergence regions as 'n' in original sequence.

[=3]: Mask Local Convergence regions in virtual sequence.

Note: The virtual sequence contains symbols only 0's and 1's.

0's indicate the Local Convergence regions corresponding

to the original DNA sequence.

Notes:

1. The -p option files the result to various formats. See the examples of -p 0, -p 1, -p 2 and -p 3 for DNA sequence U47110.

2. Any number, which is applied to or resulted by this program, referring to the positions of subject sequence starts from 0.

3. Try default values first. DNA and protein sequences are two extreme cases.