smith-waterman

There are 2 repositories under smith-waterman topic.

adrg / strutil
Golang metrics for calculating string similarity and other string utility functions
string levenshtein jaro jaro-winkler smith-waterman string-metrics string-similarity string-distance smith-waterman-gotoh string-matching dice-coefficient sorensen-dice n-gram n-gram-intersection jaccard-similarity jaccard jaccard-index overlap-coefficient hamming-distance golang
Language:Go 277
CMU-SAFARI / SneakySnake
SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.
edlib fpga gpu hardware-accelerator long-reads minimap2 needleman-wunsch pre-alignment-filtering sequence-aligner sequence-alignment short-reads smith-waterman wavefront-alignment
Language:VHDL 46
scastlara / minineedle
Needleman-Wunsch and Smith-Waterman algorithms in python
alignment algorithm needleman-wunsch smith-waterman
Language:Python 40
Martinsos / opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
sequence-alignment bioinformatics smith-waterman c-plus-plus avx alignment database-search
Language:C++ 34
lorenzocestaro / seqalign
Collection of sequence alignment algorithms.
sequence-alignment smith-waterman needleman-wunsch string-alignment string-distance hacktoberfest
Language:JavaScript 25
eriksjolund / diagonalsw
C/C++ implementation of the Smith-Waterman algorithm by using SIMD operations (e.g SSE4.1)
smith-waterman
Language:C 23
Systolic-Array-for-Smith-Waterman
jasonlin316 / Systolic-Array-for-Smith-Waterman
This work implements a dynamic programming algorithm for performing local sequence alignment. Through parallelism, it can run 136X times faster than a software running the same algorithm.
smith-waterman local sequence-alignment systolic-arrays dynamic-programming verilog short-read
Language:Verilog 19
masyagin1998 / bio-alignment
Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences
needleman-wunsch comparing-biological-sequences bioinformatics dynamic-programming hirschberg smith-waterman
Language:C 12
eriekrahman / PlagiarismDetector
A simple application to calculate similarity between two files (text document) using Smith-Waterman algorithm that is used originally to determine similar region between two sequences of DNA
golang plagiarism plagiarism-detection smith-waterman
Language:Go 11
CMU-SAFARI / Molecules2Variations
The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957
basecalling bioinformatics fast5 fasta fastq genome-analysis hifi illumina minimap2 needleman-wunsch quality-control read-mapping sam sequence-alignment sequencing smith-waterman variant-calling vcf wavefront-alignment wfa
8
althonos / pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
bioinformatics cython-library genomics needleman-wunsch python-bindings python-library sequence-alignment smith-waterman cython-wrapper simd
Language:Python 7
fjebaker / fuzzig
Fuzzy finder algorithms ala Smith-Waterman for Zig.
alignment fuzzy-finder fuzzy-search fzf smith-waterman zig
Language:Zig 7
lorenzocestaro / graphic-smith-waterman
Javascript implementation of the Smith-Waterman algorithm for sequence alignment.
smith-waterman string-alignment sequence-alignment hacktoberfest
Language:JavaScript 7
sumn2u / string-comparisons
A collection of string comparisons algorithms
javascript similarity-measures string-comparison algorithms cosine-similarity damerau-levenshtein distance hamming-distance jaccard-similarity jaro-winkler-distance levenshtein-distance smith-waterman sorensen-dice-distance string-distance trigrams
Language:JavaScript 7
lorenzoditucci / sda_examples_aws
Examples for SDAccel 2017.1+ on AWS F1 instances
sdaccel aws aws-f1 smith-waterman protein-folding examples
Language:C++ 6
Mangul-Lab-USC / review-technology-dictates-algorithms
A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.
read-alignments needleman-wunsch smith-waterman heuristics read-mapping sequence-alignment hts nanopore-sequencing illumina-sequencing pacbio-sequencing hifi-read genome-analysis
Language:Jupyter Notebook 6
pgngp / swift
GPU-based DNA sequence alignment program using Smith-Waterman
c cuda check gpu gpu-computing smith-waterman sequence-alignment multithreading
Language:Cuda 6
shehio / Computational-Biology
computational-biology smith-waterman smith-waterman-alignment gillespie-algorithm gillespie gradient-descent gradient-descent-algorithm gradient-descent-implementation genome-analysis genome-alignment differential-analysis gene-expression alternative-splicing differential-expression differential-expression-analysis single-cell-analysis single-cell-genomics viterbi-algorithm viterbi-decoder bowtie2
Language:Jupyter Notebook 6
DulanDias / DNA-Sequence-Alignment
DNA Sequence Alignment with Dynamic Programming Implementation using the Needleman-Wunsch Algorithm and Smith-Waterman Algorithm.
java sequence-alignment dna-sequences dna computational-biology bioinformatics dynamic-programming needleman-wunsch needleman-wunsch-algorithm smith-waterman smithsmith-waterman-algorithm
Language:Java 5
joergen7 / lib_dp
Dynamic Programming in Erlang.
alignment erlang needleman-wunsch similarity-score smith-waterman
Language:Erlang 5
philippvaeth / PROVAL
Comparison of Protein Sequence Embeddings to Classify Molecular Functions
bilstm deep-learning deep-neural-networks embedding protvec representation-learning skipgram smith-waterman word2vec cpcprot esm-1b protein-sequence-embeddings proval
Language:Python 5
smith-waterman-algorithm
giorgapost / smith-waterman-algorithm
A C++ implementation of the Smith - Waterman algorithm. The system consists of 3 different implementations: the one is sequential, while the other two parallelize the execution in a coarse and a fine level respectively, with the use of multithreading.
alignment-algorithms coarse-graining cplusplus cpp fine-grained multithreading omp parallel-programming smith-waterman smith-waterman-algorithm omp-parallel sequence-alignment parallel
Language:C++ 4
memaskal / sequence-alignment
A simple parallel implementation of Smith Waterman sequence alignment algorithm.
sequence-alignment smith-waterman cpp avx openmp
Language:C++ 4
mgfzemor / Pairwise-sequence-Aligment-Tool
Pairwise Sequence Aligment Tool (PSAT) a simple application to align sequences.
sequence-alignment pairwise needleman-wunsh smith-waterman needleman-wunsch-algorithm local-alignment global-alignment smith-waterman-alignment proteins amino-acids
Language:HTML 4
nanxstats / ssw-r
🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
smith-waterman sequence-alignment simd bioinformatics reticulate
Language:R 4
Enescigdem / SequenceAlignment
Global and Local Sequence Alignment
needleman-wunsch needleman-wunsch-algorithm smith-waterman smith-waterman-alignment global-alignment local-alignment bioinformatics
Language:Python 3
HLSpolito / SDAccel_kernel_cache
sdaccel high-level-synthesis cache acceleration algorithms lukas-kanade matrix-multiplication smith-waterman bitonic-sort
Language:C++ 3
kaserashi / Parallelization-of-Smith-Waterman-Algorithm
Parallel and Distributd Computing Project
pdc parallel biology gene sequence algorithm openmp c smith-waterman gene-sequence local-gene-sequncing college-project
Language:C 3
kojix2 / ruby-libssw
Fast Smith-Waterman algorithm for Ruby
smith-waterman ruby bioinformatics
Language:Ruby 3
robertaboukhalil / alignment-sandbox
Tool for exploring sequence alignment algorithms
bioinformatics genomics alignment algorithms smith-waterman needleman-wunsch webassembly
Language:Svelte 3
zenodeapp / pairwise-alignments
Solidity implementations of well-known pairwise alignment methods such as Needleman-Wunsch's global sequence alignment and the Smith-Waterman local sequence alignment algorithm.
algorithm alignment amino-acids contracts dna needleman-wunsch nucleotides proteins smith-waterman solidity substitution-matrices
Language:Solidity 3
danielfamiyeh / biothon
Biosequence analysis library
biosequences phylogenetic-dendrograms hierarchical-cluster-analysis bioinformatics clustalw clustering fasta gc-content hirschberg multiple-sequence-alignment needleman-wunsch pairwise-alignment sequence-alignment smith-waterman transcription
Language:Python 2
hewillk / aligner
Highly optimized Burrow-Wheeler Aligner specifically for Illumina ~150 bp short-read alignment.
fm-index sequence-alignment bwa bwa-mem2 smith-waterman
Language:C++ 2
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
pairwise alignment pairwise-alignment dna-sequences protein-sequences smith-waterman needleman-wunsch gotoh numba cython pypy3 python python-3-6
Language:Python 2
vic37get / smithWaterman
🔬🧬 Algoritmo de alinhamento Smith Waterman em Python
alinhamento bioinformatica python smith-waterman
Language:Python 2
ybalcanci / bioinformatics-algorithms
Bilkent University CS 481 Bioinformatics Algorithms assignments
knuth-morris-pratt exact-string-matching burrows-wheeler-transform smith-waterman needleman-wunsch rabin-karp
Language:C++ 2

smith-waterman

adrg / strutil

CMU-SAFARI / SneakySnake

scastlara / minineedle

Martinsos / opal

lorenzocestaro / seqalign

eriksjolund / diagonalsw

jasonlin316 / Systolic-Array-for-Smith-Waterman

masyagin1998 / bio-alignment

eriekrahman / PlagiarismDetector

CMU-SAFARI / Molecules2Variations

althonos / pyopal

fjebaker / fuzzig

lorenzocestaro / graphic-smith-waterman

sumn2u / string-comparisons

lorenzoditucci / sda_examples_aws

Mangul-Lab-USC / review-technology-dictates-algorithms

pgngp / swift

shehio / Computational-Biology

DulanDias / DNA-Sequence-Alignment

joergen7 / lib_dp

philippvaeth / PROVAL

giorgapost / smith-waterman-algorithm

memaskal / sequence-alignment

mgfzemor / Pairwise-sequence-Aligment-Tool

nanxstats / ssw-r

Enescigdem / SequenceAlignment

HLSpolito / SDAccel_kernel_cache

kaserashi / Parallelization-of-Smith-Waterman-Algorithm

kojix2 / ruby-libssw

robertaboukhalil / alignment-sandbox

zenodeapp / pairwise-alignments

danielfamiyeh / biothon

hewillk / aligner

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

vic37get / smithWaterman

ybalcanci / bioinformatics-algorithms