RagnarGrootKoerkamp/sassy

Fast approximate string searching

Language: Rust - Size: 281 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 23 - Forks: 1

quim0/WFA-GPU

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

Language: C - Size: 5 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 34 - Forks: 3

aziele/pairwise-sequence-alignment

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

Language: Python - Size: 44.9 KB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 13 - Forks: 3

nf-core/pairgenomealign

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

Language: Nextflow - Size: 2 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 8 - Forks: 4

pairwise-alignment/pa-generate

Generate random sequence pairs to test pairwise aligners

Language: Rust - Size: 29.3 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

pairwise-alignment/pa-bench

Benchmarking pairwise aligners

Language: Jupyter Notebook - Size: 1.19 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 36 - Forks: 1

Abrar2652/oist-comparative-genomics

Language: Python - Size: 2.36 GB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

vncsmnl/needleman-wunsch

🧬 This project implements the Needleman-Wunsch algorithm for global sequence alignment.

Language: Python - Size: 4.88 KB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

joyou159/Pairwise-Sequence-Alignment

This repository provides implementations for basic sequence alignment techniques, focusing on two popular methods: Dot Plot and Needleman-Wunsch algorithm.

Language: Python - Size: 120 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

orangeSi/bam2msa

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

Language: Crystal - Size: 10.5 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 0

iosonofabio/seqanpy

Fast pairwise sequence alignment using SeqAn, in Python.

Language: C++ - Size: 32.2 KB - Last synced at: 8 days ago - Pushed at: about 6 years ago - Stars: 13 - Forks: 7

gpmerola/SimplePairwiseAlignment

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

Language: C++ - Size: 17.6 KB - Last synced at: 10 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

BCCDC-PHL/align-compare

Pipeline to make pairwise comparisons of matched fasta sequences.

Language: Python - Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

rodriados/museqa

Multiple Sequence Aligner using hybrid parallel computing

Language: C++ - Size: 9.58 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

pairwise-alignment/pa-types

Basic types and functions for pairwise alignment.

Language: Rust - Size: 28.3 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

mrdanieleze/Genomic-Sequence-Comparison-Code-GSCC-

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!

Language: Python - Size: 26.4 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

amirezzati/bioinformatics

Intro to Bioinformatics course contents

Language: Python - Size: 50.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

marco-ruiz/pairwise-sequence-aligner

Applications that compute pairwise alignments of two biological sequences

Language: Java - Size: 1.04 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

piz2a/pairwise-alignment

Pairwise alignment algorithm testing page

Language: TypeScript - Size: 773 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

fadyehabamer/BioInformatics-SandBox

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

Size: 3.91 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Ensembl/sam-alignment-reconstructor 📦

SAM Alignment Reconstructor

Language: Python - Size: 30.3 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 1

yiliangw/marker-code-tr

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

Language: Python - Size: 3.42 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

danielfamiyeh/biothon

Biosequence analysis library

Language: Python - Size: 298 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

Amirreza-Mousavi/Protein_Normalized_SW_Similarity_Score

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.

Language: R - Size: 8.35 MB - Last synced at: 7 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

TiagoCoelhoFCUP/Bioinformatics

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

Language: Python - Size: 1.06 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

odoluca/Fast-NW-and-SW-Pairwise-alignment-using-numba-JIT

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

Language: Python - Size: 232 KB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2

Amirreza-Mousavi/Pairwise_Sequence_Alignment_Speed_Test

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.

Language: R - Size: 24.4 KB - Last synced at: 7 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

mvisani/MV_pairwise_alignment

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

Language: Python - Size: 5.86 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

gear-genomics/salt Fork of lh3/bioseq-js

Sequence Alignment Tool

Language: JavaScript - Size: 74.2 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

nhays89/ABC

Top Coder Problem

Language: Java - Size: 11.7 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0