Fast approximate string searching

GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment

Benchmarking pairwise aligners

A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

Fast pairwise sequence alignment using SeqAn, in Python.

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Basic types and functions for pairwise alignment.

Rust bindings for bsalign. A SIMD-based C library for fast partial order alignment and pairwise alignment.

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

Bioinformatics library

SAM Alignment Reconstructor

An R script that calculates a similarity matrix for a list of protein sequences with the aid of Bleakley-Yamanishi Normalized Smith-Waterman Similarity Score.

Top Coder Problem

Generate random sequence pairs to test pairwise aligners

Python implementation for DNA trace reconstruction with marker code, MIT licensed

This repository contains a simple implementation of a pairwise alignment algorithm for FASTA files using the Needleman-Wunsch algorithm.

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

Applications that compute pairwise alignments of two biological sequences

No description provided.

Intro to Bioinformatics course contents

R wrapper for running offline BLASTp alignments on curated protein sequence pairs. Originally built for personal use, now being developed into a reusable package for broader community use.

Pipeline to make pairwise comparisons of matched fasta sequences.

If protein sequence NR2F6 is very similar between humans and mice, then mice that have SNP rs11856995 might show photic sneeze reflex (PSR) phenotype.

A bioinformatics-driven assessment of Genetically Modified Organism (GMO) status in maize and soyabeans

Pairwise alignment algorithm testing page

An R script to measure the potential influence of different parameters that could have affected the speed of pairwise sequence alignment, using the functions of the Biostrings package.

Bio Informatics Lecture Notes @ Faculty of computer and information Sciences ' MU ' for the '4th Year' IT Department

This program allows to execute Pairwise alignment of proteins from a MS file.

Projects developed under the Bioinformatics college chair during the 2020/2021 school year