StarAlignmentTool.h - The class StarAlignmentTool aligns multiple sequences taking individual alignments as input using the star alignment method. Sequence.h - The class Sequence is used to hold a single DNA sequence. This feature allows one to take a matrix of nucleotides, and an existing alignment of their. Can be edited for different scoring method. Aligning nucleotide sequences to match an amino acid alignment. ScoringScheme.txt - Contains data used by the AlignmentTool class for scoring.
ALIGN DNA SEQUENCES HOW TO
LENGTH 7 minutes Simulate Agarose Gel Electrophoresis INSIDE THE VIDEO Learn how to simulate agarose gel electrophoresis to predict bands on a gel following restriction digest or PCR amplification. MSATool.cpp - Main program that reads sequences from input file, uses AlignmentTool and StarAlignment to align them and writes output to the provided output file. INSIDE THE VIDEO Align DNA sequences with a reference sequence to verify cloning or mutagenesis, or to align cDNA to a chromosome. Input and output files have to be provided as arguments.Īlignment.h - Class Alignment holds data for two DNA sequences.ĪlignmentTool.h - The class AlignmentTool is used to align two individual sequences.ĭynamicSafe2DArray - Templatized wrapper class for 2D arrays.ĭynamicSafeArray - Tempatized wrapper class for arrays. The program can be run from the command line. I developed this project as part of my course in data structures taken in Fall 2007. For k sequences, star alignment method provides a more efficient heuristic method of aligning sequences. Optimally aligning k sequences using the same algorithm has exponential complexity. Optimally aligning two sequences of length n has a time complexity of O(n^2) (see Needleman-Wunsch algorithm: ).
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