Alignment of DNA

This project is a school assignment described in PI421_biologie.pdf. The goal of this project it to compute the best alignment of two sequence of DNA under the consideration the gap penality. My classmate and I have implemented the Gotoh's Algorithm with Java. The source codes are in the folder PI_bio/src/workspace and the test DNA sequence data are in PI_bio/SubSeq_Res{52,320,3275}.txt.

Explanation the utility of each file in PI_bio/src/workspace

• ReadFile.java is for read a file with DNA sequence data format like SubSeq_Res{52,320,3275}.txt
• Common_sequence.java is for calculate the longest common sequence of two strings.
• Type_Result.java is for customize the type of result of common_sequence.
• Refline_alignement.java is for calculate the alignement with score difined in Blosum50.java.
• Keyword_tree.java is for construct the type keyword tree.
• Search_tool.java is a tool to find the local alignement.