needleman-wunsch
Here are 73 public repositories matching this topic...
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
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May 20, 2024 - Python
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.o…
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Mar 31, 2023 - VHDL
Needleman-Wunsch and Smith-Waterman algorithms in python
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Mar 20, 2024 - Python
Interactive Visualization of Needleman-Wunsch Algorithm in Javascript
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Apr 3, 2019 - JavaScript
Collection of sequence alignment algorithms.
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Mar 6, 2023 - JavaScript
Generate an accurate, timestamped transcript given an audio file and its text using Google Cloud's Speech-to-Text API via gRPC.
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Aug 16, 2020 - Swift
Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.
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Jul 10, 2018 - Python
Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences
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Dec 7, 2019 - C
Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.
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Aug 29, 2020 - C
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.
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Apr 7, 2021 - Jupyter Notebook
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…
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Jun 14, 2022
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
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May 15, 2024 - Python
Use the Needleman-Wunsch algorithm to align two sequences: s1 and s2. Assume that a match = +2, mismatch = -2, gap = -2
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Jun 22, 2020 - Python
🔬 🏁 Comparison of DNA Sequences
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Aug 13, 2020 - C++
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.…
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Jul 7, 2021 - Jupyter Notebook
Sequence alignment algorithms
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Feb 9, 2019 - Go
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Nov 9, 2020 - Python
Dynamic Programming in Erlang.
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Aug 10, 2017 - Erlang
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)
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Jun 26, 2017 - Python
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