Implementation of BLAST(Basic Local Alignment Search Tool) algorithm in Python 3.5 using Numpy.
This code can provide you with a glimpse of how BLAST works and how it can actually be realised in code.
This BLAST search is based on nucleotide-nucleotide search. Amino acid search using PAM scoring matrices will soon be provided on this repository.
Sorry for lack of comments in the source code. This change will also be done soon.
hsp.py : Actual file with the code.
word.py : File with the code implementing only w-mers fragmentation part.
query.txt : File consisting of dummy sequence of E.Coli genome.
assembly.txt : File consisting of database sequence of a part of E.Coli genome. As this algorithm has a time complexity of o(n^2), it is not possible to run a database search of actual genomic sequence on personal computers.