needleman-wunsch

There are 0 repository under needleman-wunsch topic.

• kensho-technologies / sequence_align

  Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

  hirschbergneedleman-wunschpyo3pythonrustsequence-alignmentbioinformaticsnatural-language-processingnlp
  Language:Python 63

• jonblack / cmpgpx

  Show the differences between GPX files

  gpxalignmentneedleman-wunsch
  Language:Python 61

• 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.

  sequence-alignerfpgagpuhardware-acceleratorminimap2edlibsmith-watermanneedleman-wunschpre-alignment-filteringsequence-alignmentlong-readsshort-readswavefront-alignment
  Language:VHDL 47

• scastlara / minineedle

  Needleman-Wunsch and Smith-Waterman algorithms in python

  alignmentalgorithmneedleman-wunschsmith-waterman
  Language:Python 44

• drdrsh / Needleman-Wunsch

  Interactive Visualization of Needleman-Wunsch Algorithm in Javascript

  needleman-wunschjavascriptalignment
  Language:JavaScript 42

• lorenzocestaro / seqalign

  Collection of sequence alignment algorithms.

  sequence-alignmentsmith-watermanneedleman-wunschstring-alignmentstring-distancehacktoberfest
  Language:JavaScript 25

• lukereichold / SpeechTimestamper

  Generate an accurate, timestamped transcript given an audio file and its text using Google Cloud's Speech-to-Text API via gRPC.

  natural-language-processingnlpaudio-transcribingspeech-to-texttimestampgrpcgcpstring-alignmentneedleman-wunschgoogle-cloud-platformkaraokeprotobuftranscriptiongcp-speechkaraoke-maker
  Language:Swift 19

• mmtechslv / nwunch

  Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.

  needleman-wunschneedleman-wunsch-algorithmbioinformaticsalignmentsequence-alignmentalignment-algorithmpythondemo
  Language:Python 13

• masyagin1998 / bio-alignment

  Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences

  needleman-wunschcomparing-biological-sequencesbioinformaticsdynamic-programminghirschbergsmith-waterman
  Language:C 12

• oboes / gotoh

  Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.

  needleman-wunschalignmentbioinformaticsdynamic-programming
  Language:C 9

• althonos / pyopal

  Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

  bioinformaticscython-librarygenomicsneedleman-wunschpython-bindingspython-librarysequence-alignmentsmith-watermancython-wrappersimd
  Language:Python 8

• bharath3794 / Algorithms-Illuminated---Part-3

  This is the implementation of 3rd Part in 3-Part Series of Algorithms Illuminated Book. All Implementations in this repository are written in both Python and Golang. Single IPython Notebook contains all Algorithms given in this Part 3.

  greedy-algorithmshuffman-algorithmprims-algorithmkruskal-algorithmunion-finddisjoint-setknapsack-problemweighted-independent-setneedleman-wunschoptimal-binary-search-treebellman-ford-algorithmfloyd-warshall-algorithmalgorithms-illuminateddynamic-programmingprim-algorithmgolangpythoncoursera-algorithms-specialization
  Language:Jupyter Notebook 8

• 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

  basecallingbioinformaticsfast5fastafastqgenome-analysishifiilluminaminimap2needleman-wunschquality-controlread-mappingsamsequence-alignmentsequencingsmith-watermanvariant-callingvcfwavefront-alignmentwfa
  8

• abdullahmujahidali / Bio-Infomatics

  Use the Needleman-Wunsch algorithm to align two sequences: s1 and s2. Assume that a match = +2, mismatch = -2, gap = -2

  python3pythonbioinformaticsneedleman-wunschneedleman
  Language:Python 6
• affine-gaps

  ashvardanian / affine-gaps

  Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment

  bioinformaticsproteinprotein-sequencessequence-alignmentjitlevenshtein-algorithmlevenshtein-distanceneedleman-wunschsearchsmith-watermanstring-search
  Language:Python 6

• DulanDias / DNA-Sequence-Alignment

  DNA Sequence Alignment with Dynamic Programming Implementation using the Needleman-Wunsch Algorithm and Smith-Waterman Algorithm.

  javasequence-alignmentdna-sequencesdnacomputational-biologybioinformaticsdynamic-programmingneedleman-wunschneedleman-wunsch-algorithmsmith-watermansmithsmith-waterman-algorithm
  Language:Java 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-alignmentsneedleman-wunschsmith-watermanheuristicsread-mappingsequence-alignmenthtsnanopore-sequencingillumina-sequencingpacbio-sequencinghifi-readgenome-analysis
  Language:Jupyter Notebook 6

• Pawan300 / Bioinformatics

  bioinformaticsneedleman-wunschsmithwaterdotplotslidingwindow
  Language:Python 6

• psykhi / sequencing

  Sequence alignment algorithms

  bioinformaticsneedleman-wunschsequence-alignmentlevenshtein-distancegolanggo
  Language:Go 6

• zumrudu-anka / cpp-openmp-needleman-wunsch

  :microscope: :checkered_flag: Comparison of DNA Sequences

  needleman-wunsch-algorithmneedleman-wunschneedlemanwunschopenmpcpp
  Language:C++ 6

• benhid / NeedlemanWunschPy

  This code is meant for educational purposes only! Sequence alignment in Python 3.x using Needleman–Wunsch algorithm. Reference code from TyMA (2017 - University of Málaga)

  bioinformaticssequence-alignmentsneedleman-wunsch
  Language:Python 5

• joergen7 / lib_dp

  Dynamic Programming in Erlang.

  alignmenterlangneedleman-wunschsimilarity-scoresmith-waterman
  Language:Erlang 5

• SleekPanther / sequence-alignment

  Sequence Alignment (Needleman–Wunsch Algorithm using Dynamic Programming) for aligning sequences (words, sentences, DNA etc.)

  dynamic-programmingdynamicpseudocodeoptimal-substructureoptimaloptimalityneedleman-wunschneedlemanwunschneedlemanwunschalgorithmalgorithmsalgorithm-designmemoizationmemomemorizationnoah-patullonoahpatullopatulo
  Language:Java 5

• mstfymrtc / NeedlemanWunsch

  C# implementation of Needleman-Wunsch global sequence alignment algorithm.

  sequence-alignmentneedleman-wunschdynamic-programmingglobal-alignment
  Language:C# 4

• Enescigdem / SequenceAlignment

  Global and Local Sequence Alignment

  needleman-wunschneedleman-wunsch-algorithmsmith-watermansmith-waterman-alignmentglobal-alignmentlocal-alignmentbioinformatics
  Language:Python 3

• FrancisLawlor / NeedlemanWunsch

  An implementation of the Needleman-Wunsch algorithm for finding the best global alignment of two nucleotides.

  bioinformaticsneedleman-wunschdynamic-programming
  Language:Java 3

• hanaecarrie / genetics-multiple-alignment

  star alignment method implementation for multiple DNA sequences alignment

  geneticsalignmentneedleman-wunschdna-sequences
  Language:Jupyter Notebook 3

• hernanmd / class-diff

  A Pharo classes comparer

  classescomparison-toolneedleman-wunschpharopharo-smalltalksmalltalk
  Language:Smalltalk 3

• huutuongtu / MDD-Metric

  This is Mispronunciation detection and diagnosis Score Metric

  dynamic-programmingmddneedleman-wunschmdd-metricmispronunciation-detectionmispronunciation-detection-metric
  Language:Python 3

• lozaeric / pymsearch

  Este es un simple buscador que permite encontrar palabras clave similares a una palabra buscada. Para realizar esto, verifica los caracteres que coinciden entre ambas utilizando el algoritmo Needleman-Wunsch.

  search-enginesearch-algorithmphp5needleman-wunschsearching
  Language:PHP 3

• pityka / pairwisealignment

  pairwise sequence alignment in scala

  needleman-wunschsmith-waterman-gotohwavefront-alignmentscala
  Language:Scala 3

• robertaboukhalil / alignment-sandbox

  Tool for exploring sequence alignment algorithms

  bioinformaticsgenomicsalignmentalgorithmssmith-watermanneedleman-wunschwebassembly
  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.

  algorithmalignmentamino-acidsdnaneedleman-wunschnucleotidesproteinssmith-watermansubstitution-matricescontractssolidity
  Language:Solidity 3

• Howeng98 / Smith_Waterman_parallel

  Implement parallel Smith Waterman algorithm on CUDA

  smith-waterman-alignmentsmith-waterman-algorithmsmith-watermanneedleman-wunschneedleman-wunsch-algorithmcuda-programmingcudaparallel-programming
  Language:Cuda 2

• mamutalib / Bio-informatics

  Bio informatics course materials for NEUB students.

  edit-distance-algorithmneedleman-wunsch-algorithmneubsmith-waterman-algorithmdna-transcriptionpdppartial-digest-problembio-informaticsbioinformaticsbioinformatics-algorithmsalgorithmedit-distanceedit-distance-algorithm-implementationedit-distance-algorithmsneedleman-wunschneedleman-wunsch-alignmentneedleman-algorithm
  Language:C++ 2

• sirineFoudili / DNA-comparison-and-alignment-

  web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.

  dnaadnalignementalignmentalignment-freeindexationbloom-filterk-mershashingphylogenetic-treephylogeniedna-alignmentneedleman-wunschflaskpythonbioinformaticsbioinformatique
  Language:JavaScript 2