SeqEntropy Files

2.0.1 README - 20130203
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 * Sequence Read Entropy
 *
 * Copyright (c) Hsueh-Ting Chu
 * 4F., No.286, Defu Rd., South Dist., Taichung City 402, Taiwan.
 * All rights reserved.
 *
 * This file is a part of the Sequence Read Entropy Program.
 * The use and distribution terms for this software are covered by the
 * Common Public License 1.0 (http://opensource.org/licenses/cpl1.0.php).
 * By using this software in any fashion, you are agreeing to be bound by
 * the terms of this license. You must not remove this notice, or
 * any other, from this software.
 * 2.0.1 Beta 2013/01/11 HTChu
 * 
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(1) Quick usage
Using E. coli str. K-12 substr. MG1655 chromosome NC_000913.fa:

(1.a) Demo command:
  (Windows) SeqReadEntropy SeqReadEntropy NC_000913.fa 35

(1.b) parameters 
     SeqReadEntropy sequecne_file(.fa) read_Length

(1.c) Output:
    Entropy (9114118/9279282)of Length= 35 = 6.95184240948066 = 6.96751437325532 = 0.224929048367957%
    The result indicates the genome of the E. coli strain will lose 0.22% entropy if it is sequenced with reads of length=35bp.

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(2) Multiple sequence files for big genomes such as human genome
using the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome)
avaialable at http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
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(2.a) Demo command:
  (Windows)   SeqReadEntropy *.fa 100 5

(2.b) parameters 
    EBARDenovo multiple_sequecne_file(*.fa) read_Length clusters(N)
    Divide the computation into 4^N times.

(2.c) Output:
    Entropy (5591277928/5722624360)of Length= 100 = 9.73162717417607 = 9.75759523922774 = 0.266131812347326%
    The result indicates the genome of the human genome will lose 0.26% entropy if it is sequenced with reads of length=100bp.
    
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(3) Sequence Read Repeat
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(2.a) Demo command:
  (Windows)   SeqReadRepeat *.fa 100 5

(2.b) parameters 
    EBARDenovo multiple_sequecne_file(*.fa) read_Length clusters(N)
    Divide the computation into 4^N times.

(2.c) Output:
    (Repeats=118 AllReads=252222)of Length= 30 = 0.0467841821887068%
    The result indicates the genome of the genome will have 0.047% repeats if it is sequenced with reads of length=100bp.