williamgilpin/pypdb

A Python API for the RCSB Protein Data Bank (PDB)

Language: Python - Size: 613 KB - Last synced: about 13 hours ago - Pushed: about 17 hours ago - Stars: 297 - Forks: 75

gauravcodepro/miniprot-protein-annotator

from protein alignments to deep learning preparatory.

Language: Python - Size: 74.2 KB - Last synced: about 6 hours ago - Pushed: about 21 hours ago - Stars: 0 - Forks: 0

fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Language: Python - Size: 3.58 MB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 24 - Forks: 4

bioinf-mcb/Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Language: Python - Size: 6.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 29 - Forks: 6

pymodproject/pymod

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

Language: Python - Size: 1.69 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 69 - Forks: 19

soldamatlab/DESilico.jl

Directed Evolution in Silico

Language: Julia - Size: 81.1 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

gauravcodepro/proteinalignment-annotation-gem

a ruby gem for protein alignments. index the protein alignments, extract the regions of interest, extract the locus, extract the dimensions.

Language: Ruby - Size: 45.9 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

songlab-cal/tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

Language: Python - Size: 840 KB - Last synced: 4 days ago - Pushed: over 1 year ago - Stars: 631 - Forks: 129

naity/protein-transformer

Implement, train, tune, and evaluate a transformer model for antibody classification with this step-by-step code.

Language: Jupyter Notebook - Size: 22.9 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 2

nanxstats/Rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

Language: R - Size: 10.3 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 35 - Forks: 12

nanxstats/protr

🧬 Toolkit for generating various numerical features of protein sequences

Language: R - Size: 8.86 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 51 - Forks: 12

burkesquires/FeaVar

A python package to compute clusters of sequence feature variant types (SFVTs) based upon user-selected subsequence.

Language: Clarion - Size: 1.85 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 3 - Forks: 0

sacdallago/bio_embeddings

Get protein embeddings from protein sequences

Language: HTML - Size: 68.3 MB - Last synced: 2 days ago - Pushed: about 1 year ago - Stars: 438 - Forks: 62

KCLabMTU/LMCrot

Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified Site Predictor

Language: Python - Size: 22.5 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 2

gauravcodepro/protein-annotator

python package to analyze the protein coding regions for the genome annotation. It uses the miniprot for the alignment and gives you all the protein predicted mRNA, coding regions and other exon positions.

Language: Python - Size: 62.5 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

gauravcodepro/coding-stitcher-pangenome

a coding sticher for genome annotations, which stitch all your coding regions coming out of the exon alignments and will produce the gene visualization for the pangenome

Language: Python - Size: 28.3 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

microsoft/evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Language: Python - Size: 18.3 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 425 - Forks: 57

gauravcodepro/mRNAplotter

plotting tools for the mRNA from the proteome to the genome anntoation. Produces a tab delimited files with the start and the stop of the mRNAs

Language: Python - Size: 10.7 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

gauravcodepro/codingplotter

a coding plotter for the protein annotations coming from the annotation of the genome using the protein hints and to extract and plot the specific length estimates.

Language: Python - Size: 24.4 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

gauravcodepro/intergenic-extractor

extracting all the intergenic regions from the genome annotation using the protein alignments.

Language: Python - Size: 52.7 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

gauravcodepro/genome-annotation-visualizer

a R function part to visualizae the genes coming from the genome alignment proteome annotations. This is a part of the evoseq R package

Language: R - Size: 37.1 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

jjerphan/CS5242Project 📦

Predicting Protein – Ligand Interaction by using Deep Learning Models

Language: Python - Size: 25.6 MB - Last synced: 15 days ago - Pushed: over 5 years ago - Stars: 3 - Forks: 2

lucidrains/protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

Language: Python - Size: 37.1 KB - Last synced: 14 days ago - Pushed: almost 3 years ago - Stars: 145 - Forks: 24

oxpig/AbLang

AbLang: A language model for antibodies

Language: Python - Size: 74.2 KB - Last synced: 11 days ago - Pushed: 8 months ago - Stars: 103 - Forks: 24

J-SNACKKB/FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

Language: Jupyter Notebook - Size: 595 MB - Last synced: 2 days ago - Pushed: 11 months ago - Stars: 84 - Forks: 12

grimmlab/ProLaTherm

Protein Language Model-based Protein Thermophilicity Prediction

Language: Python - Size: 27.6 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Language: Java - Size: 48.1 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 574 - Forks: 376

chey97/ProteinSeq_Classifier

Proteins have different family types, this modal determine a protein's family type based on sequence. Inspired by search engines such as BLAST which has this capability, but it want to try out and see if a machine learning approach can do a good job in classifying a protein's family based on the protein sequence.

Language: Python - Size: 5.22 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

OpenProteinAI/PoET

Inference code for PoET: A generative model of protein families as sequences-of-sequences

Language: Python - Size: 772 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 22 - Forks: 2

ChakradharG/PeptideBERT

Transformer Based Language Model for Peptide Property Prediction

Language: Python - Size: 40 KB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 22 - Forks: 8

mims-harvard/SPECTRA

Spectral Framework For AI Model Evaluation

Language: Roff - Size: 70 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 13 - Forks: 1

gozsari/ProtFeat

ProtFeat is protein feature extraction tool that utilizes POSSUM and iFeature.

Language: Python - Size: 125 MB - Last synced: 1 day ago - Pushed: 3 months ago - Stars: 15 - Forks: 0

flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

Language: Python - Size: 56.7 MB - Last synced: 23 days ago - Pushed: about 1 month ago - Stars: 96 - Forks: 16

aws-samples/amazon-sagemaker-protein-classification

Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.

Language: Jupyter Notebook - Size: 108 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 40 - Forks: 23

psipred/protein-vae

Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies

Language: Python - Size: 27.3 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 75 - Forks: 17

nf-core/proteinfold

Protein 3D structure prediction pipeline

Language: Nextflow - Size: 5.58 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 41 - Forks: 27

naity/finetune-esm

Scalable Protein Language Model Finetuning with Distributed Learning and Advanced Training Techniques such as LoRA.

Language: Jupyter Notebook - Size: 4.42 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

HobnobMancer/cazy_webscraper

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

Language: Python - Size: 46.6 MB - Last synced: 27 minutes ago - Pushed: about 2 months ago - Stars: 13 - Forks: 3

kyegomez/Progen

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

Language: Python - Size: 218 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 7 - Forks: 0

LirongWu/awesome-protein-representation-learning

Awesome Protein Representation Learning

Size: 166 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 531 - Forks: 62

hrzn/prot-gpt

Nano Prot GPT: NanoGPT on protein sequences

Language: Jupyter Notebook - Size: 1.12 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 17 - Forks: 1

AstraBert/resistML

A tool for AMR gene family prediction, simple and ML-based

Language: Jupyter Notebook - Size: 1.54 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

d8vela/ColabSeq

ColabSeq: The one-stop shop for all of your multiple sequence analysis needs.

Language: Jupyter Notebook - Size: 402 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

tusharpandey003/FASTA-Sequence-Analysis-Web-App

Analysis of FASTA ,Protein,DNA sequence.

Language: Python - Size: 28.3 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

ChakradharG/IDP-BERT

Property Prediction for Intrinsically Disordered Proteins (IDPs) using Language Model

Language: Python - Size: 151 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

pgarrett-scripps/ProteinCleaverStreamlitApp

Protein Cleaver is a versatile tool for protein analysis and digestion.

Language: Python - Size: 748 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

whitehead/plaac

Prion-Like Amino Acid Composition

Language: Java - Size: 15.8 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 15 - Forks: 8

BoHuangLab/CELL-E_2

Encoder-only model for image-based protein predictions

Language: Python - Size: 12.9 MB - Last synced: 23 days ago - Pushed: 5 months ago - Stars: 8 - Forks: 0

seqan/lambda

LAMBDA – the Local Aligner for Massive Biological DatA

Language: C++ - Size: 2.26 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 74 - Forks: 19

VerisimilitudeX/DNAnalyzer

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Language: Java - Size: 188 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 125 - Forks: 55

jithin8mathew/Protein-feature-extraction

Python code to extract features from Protein sequences for Machine Learning/Deep Learning

Language: Python - Size: 1.56 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 17 - Forks: 2

PNNL-Comp-Mass-Spec/protein-coverage-summarizer

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

Language: C# - Size: 34.8 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 3

amckenna41/protPy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

Language: Python - Size: 255 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 7 - Forks: 0

guyleonard/get_jgi_genomes

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Language: Perl - Size: 86.9 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 27 - Forks: 5

HySonLab/Protein_Pretrain

Multimodal Pretraining for Unsupervised Protein Representation Learning

Language: Python - Size: 216 KB - Last synced: 2 days ago - Pushed: 5 months ago - Stars: 9 - Forks: 0

vrettasm/PyCamcoil

Provides a Python implementation of the camcoil program (originally written in C) to estimate the random coil chemical shift values from a sequence (string) of amino-acids.

Language: Python - Size: 318 KB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

glezdiazh/MINDPROT

MINDPROT: Markov Inside for Drugs and Proteins

Language: Python - Size: 24.9 MB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

Language: Jupyter Notebook - Size: 2.06 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 7 - Forks: 5

ProteinEngineering-PESB2/RUDEUS

Developing classification models for DNA-Binding proteins through machine learning and large language models

Language: Jupyter Notebook - Size: 18 MB - Last synced: about 21 hours ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

PKU-YuanGroup/TaxDiff

The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"

Language: Python - Size: 2.63 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 20 - Forks: 1

ShutaoChen97/IIDL-PepPI

Progressive Transfer Learning for Peptide-Protein-Specific Interaction Profiling based on Interpretable Biological Sequence Pragmatic Analysis

Language: Python - Size: 47.8 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 2

RudoRoemer/PDB2MovieWeb

Web-based front- and backend for PDB2Movie scripts

Language: PHP - Size: 14.8 MB - Last synced: 3 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

microsoft/protein-uq

Benchmarking uncertainty quantification methods on proteins.

Language: Shell - Size: 131 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 17 - Forks: 1

dosorio/Peptides

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Language: R - Size: 5.68 MB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 73 - Forks: 21

univieCUBE/deepnog

Protein orthologous group assignment with deep learning

Language: Python - Size: 4.51 MB - Last synced: 10 days ago - Pushed: about 1 year ago - Stars: 24 - Forks: 8

Pathmanaban/ProtMapPep

Map the peptides to its corresponding protein sequence and locate the modification sites

Language: Python - Size: 7.18 MB - Last synced: 3 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

prescient-design/walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

Language: Python - Size: 57.6 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 1

YSChen0609/Sequence-Align

A sequence alignment module implementing Needleman-Wunsch algorithm.

Language: Python - Size: 7.81 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

debbiemarkslab/plmc

Inference of couplings in proteins and RNAs from sequence variation

Language: C - Size: 979 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 94 - Forks: 36

sbl-sdsc/mmtf-pyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Language: Python - Size: 524 MB - Last synced: 18 days ago - Pushed: about 1 year ago - Stars: 67 - Forks: 27

fteufel/SecretoGen

A conditional generative model for signal peptides

Language: Python - Size: 964 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1

guillecarrillo/proteoparc

A pipeline for the creation of protein databases focused on paleoprotein mass spectrometry identification

Language: Python - Size: 621 KB - Last synced: 3 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

pgarrett-scripps/FastaFrames

Python package to convert between FASTA files and Pandas DataFrames.

Language: Python - Size: 43 KB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 0

ikmb/vcf2prot

Accelerate the generation of personalized proteomes from a Variant calling format (VCF) file and a reference proteome using graphical processing units (GPUs).

Language: Rust - Size: 39.6 MB - Last synced: 25 days ago - Pushed: about 1 year ago - Stars: 11 - Forks: 1

kklemon/ProtEnc

Extract protein embeddings the easy way.

Language: Python - Size: 117 KB - Last synced: 7 days ago - Pushed: 7 months ago - Stars: 4 - Forks: 0

graph-part/graph-part

A biological sequence data partitioning method

Language: Jupyter Notebook - Size: 46.3 MB - Last synced: 5 days ago - Pushed: 7 months ago - Stars: 19 - Forks: 4

dohlee/abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

Language: Jupyter Notebook - Size: 154 KB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

Bitbol-Lab/DiffPALM

Differentiable Pairing using Alignment-based Language Models

Language: Jupyter Notebook - Size: 2.82 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 10 - Forks: 2

Protein-Engineering-Framework/PyPEF

PyPEF – Pythonic Protein Engineering Framework

Language: Python - Size: 42 MB - Last synced: 25 days ago - Pushed: 4 months ago - Stars: 18 - Forks: 3

danielathome19/ProteiNN-Structure-Predictor

A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.

Language: Python - Size: 9.7 MB - Last synced: 14 days ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

songlab-cal/tape-neurips2019

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

Language: Python - Size: 136 KB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 115 - Forks: 34

ziegler-ingo/cleavage_benchmark

Code and dataset for paper "Proteasomal cleavage prediction: state-of-the-art and future directions"

Language: Python - Size: 50.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

zenodeapp/substitution-matrices

A CRUD for substitution matrices like BLOSUM50, BLOSUM62, PAM250 and more; commonly used in Bioinformatics and Evolutionary Biology.

Language: Solidity - Size: 128 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

kalyaniasthana/consensus_design_pipeline_old

Language: Python - Size: 149 MB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

D-K-Deng/Protein_Optimize

A software tool designed for protein optimization, ProteinOpti integrates sequence manipulation with structural analysis, streamlining the generation, prediction, and evaluation of protein variants using Google Colab.

Language: Jupyter Notebook - Size: 1.1 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 5 - Forks: 0

linudz/caastools

CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.

Language: Python - Size: 4.75 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 8 - Forks: 1

anocca-ab/sequence-viewer

A DNA and protein sequence viewer developed and maintained by Anocca

Language: TypeScript - Size: 2.64 MB - Last synced: 17 days ago - Pushed: 4 months ago - Stars: 6 - Forks: 2

dohlee/antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

Language: Jupyter Notebook - Size: 228 KB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 22 - Forks: 5

ericmjl/flu-sequence-predictor

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

Language: Jupyter Notebook - Size: 120 MB - Last synced: 15 days ago - Pushed: 9 months ago - Stars: 36 - Forks: 12

xduan7/bioseq-learning

deep learning experiments on biological sequences with PyTorch

Language: Python - Size: 339 MB - Last synced: 18 days ago - Pushed: about 3 years ago - Stars: 6 - Forks: 1

labstructbioinf/DeepCoil

Fast and accurate prediction of coiled coil domains in protein sequences. ​

Language: Python - Size: 154 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 1

feliixx/gotranseq

convert nucleic sequence in protein sequence

Language: Go - Size: 3 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 17 - Forks: 9

MR-SIR2525/fasta-sequence-counter

counter.py: A simple nucleotide sequence counter that cross references fasta files with sequences from a input txt file.

Language: Python - Size: 9.77 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

conradry/pytorch-rgn

Recurrent Geometric Network in Pytorch

Language: Jupyter Notebook - Size: 79.1 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 28 - Forks: 13

amaurypm/pseqsid

Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.

Language: Rust - Size: 81.1 KB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 1

niklases/PyPEF

PyPEF – Pythonic Protein Engineering Framework

Language: Python - Size: 41.7 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 8 - Forks: 2

zaidalrakabi/SeqKernel

String Kernel for comparing protein sequences

Language: C++ - Size: 670 KB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

sbl-sdsc/mmtf-spark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Language: Java - Size: 1.57 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 22 - Forks: 35

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: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2

nanxstats/protrweb

Shiny Web Application for Protein Sequence-Derived Descriptor Computation

Language: HTML - Size: 763 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 3