项目作者: HazarZYGC

项目描述 :
An algorithm for solving protein sequence alignment which aims to find optimum matching between two amino acid sequences
高级语言: Java
项目地址: git://github.com/HazarZYGC/Protein-Sequence.git
创建时间: 2020-06-19T13:21:50Z
项目社区:https://github.com/HazarZYGC/Protein-Sequence

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Protein-Sequence

I developed an algorithm for solving protein sequence alignment
which aims to find optimum matching between two amino acid sequences.

Inputs are: two given strings x, y where length(x)=m and length(y)=n, and a cost matrix C which prescribes a
cost for matching and mismatching characters. A gap penalty is the component deducted from
alignment score due to the presence of a gap, i.e., matching of a letter in one sequence with a
dash (space) in the other sequence. A gap penalty may be a function of the length of the gap;
for example, a linear gap penalty is a constant g such that each inserted or deleted symbol is
charged g; the total cost of a gap of length L is equal to gL.

Input:

1.Two protein strings x and y, each one is in one line of the file (at most 1000 amino acid)

2.Cost matrix (BLOSUM62 scoring matrix)

3.Linear gap penalty equal to -5 (i.e., a cost of -5 is assessed for each gap symbol)

Output:

1.The maximum alignment score between x and y.

2.Best alignment between x and y.