Files in this Repository:
- blosum/ Adjusted BLOSUM source code from the original Henikoff paper, updated to make it work
- protomat/ Adjusted Protomat source code from the original Henikoff paper, updated to make it work
- 1234.txt results from homologsearch.py for seed 1234
- 5678.txt results from homologsearch.py for seed 5678
- 9001.txt results from homologsearch.py for seed 9001
- astral-scopedom-seqres-gd-sel-gs-bib-49-2.06.fa sequences from the Astral database for testing
- blosum62.csv results for blosum62
- blosum62.mat the BLOSUM62 matrix used in NWalign
- homologsearch.py runs NW comparisons and generates confusion matrices for each substitution matrix
- iij2mat.py converts files output by blosum.c into format readable by NWalign
- makefile makefile for NWalign.cpp
- new99.csv results for new99
- new99.mat our new generated matrix used in NWalign
- NWalign.cpp Needleman-Wunsch alignment implemented in C++ for efficiency
- NWalign.h header file for NWalign.cpp
- NWalign.py original NW implementation from which NWalign.cpp was made
- randblos.csv results for randblos
- randblos.mat randomly generated substitution matrix based off of BLOSUM62
- randblos.py randomly generates a subsitution matrix given value frequencies present in BLOSUM62
- README.md this file
- seeds.txt the three seeds used to run triplicate
- tests.R R script that generates mean accuracy, precision, and recall and performs t-tests of all these parameters between the three matrices