How-to-Use



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

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

SbjFileName ........: File contains FASTA-formated subject sequences.
OutputFileName .....: File for text output.

OPTIONS:
-b Base ............: Number of NTs' as a motif.
-t MotifsInSeed ....: # of motifs in a seed.

-x MotifScore ......: Score for a matched motif.
-y mismatchedScore .: Score for a mismatched NT.
-v Threshold .......: Minimum value to accept a window.
-w WindowSize ......: Window size.
-f ExtendedWindows .: Number of extended Windows to be accepted.

-c CutoffScore .....: Minimum Score to accept this found segment.
-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. -t option gives a barrier to initiate a motif search. -t 1 has no restriction, but -t 4 requires an occurrence of four consecutive and identical motifs in a subject sequence.

  2. -x, -y and -v options provide a rule for further extensions if on a window.

  3. -w option shows the size of a motif observation. -w 16 gives a window size 16 as the following fashion where X=”tga”.

    DNA Segment: ...tgatgaaatgagatgaaatgaaatgatgaa...
    Window: ........XXaaXgaXaaXaaXXa...

  4. 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 as the options -b 2 -t 2 -x 3 -y -1 -v 0 -w 16 -f 1.

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