Giter Club home page Giter Club logo

blast-python's Introduction

BLAST-Python

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.

File-Description:

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.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.