This is a amplement of Smith-Waterman algorithm, maintaned by: Mingpeng Wang(1511212) wmpeng@outlook.com
For more information about this homework please visit github repository https://github.com/wmpeng/DataScienceHomework (that will be visible at 24:00, July 5th.)
homework
├── DataScienceHomework vs2015 porject
│ ├── DataScienceHomework
│ │ └ smithWaterman.cpp source code file
│ └── DataScienceHomework.sln
├── DataScienceHomework.exe executable file of release version
├── A.txt sample file : the first DNA sequence file
├── B.txt sample file : the second DNA sequence file
├── S.txt sample file : score matrix and gap penalty file
└── README.md
My homework include a Vistual Studio 2015 project folder, a An executable file, three parameter files named "A.txt", "B.txt", "S.txt", and a readme file that you are reading.
The source code's path is ".\DataScienceHomework\DataScienceHomework\smithWaterman.cpp".
The executable file is "DataScienceHomework.exe".
The process can run without installation.
You can run the executable file in Powershell by command line like this : DataScienceHomework <1stFile> <2ndFile> <3rdFile>
<1stFile> and <2ndFile> are the first and the second DNA sequences file that only contain upper case letter {A,T,G,C} (line breaks are allowed).
<3rdFile> talls the scoring matrix and gap penalty ,whose format likes that：
scoreMatrix:
A T G C
A 1 -2 -2 -2
T -2 1 -2 -2
G -2 -2 1 -2
C -2 -2 -2 1
GapPenalty:
-2
↑ When the SingleGapPenalty isn't define ,which is default ↑
scoreMatrix:
...
GapPenalty:
-1 -2 -3 -4
↑ When the SingleGapPenalty isn't define ,which is default ↑
The result will be output at screen. When the the parameter files are the sample files (different and gap -2, the same +1), the result is :
highest value is 18.000000
sequences 1 from 1758 to 1784 : GAAGTTGAGCACGTAAGGCCTACGTTC
sequences 2 from 2004 to 2030 : GAAGTTGAGCACGTGATGCCTAAGTTC
Contact me at anytime :
github https://github.com/wmpeng/DataScienceHomework
email wmpeng@outlook.com