Top 10 protein-sequence Open-Source Projects

• tape

  1 620 0.0 Python

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

  

• BioJava

  2 575 8.2 Java

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

  

Project mention: Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo | news.ycombinator.com | 2024-02-08

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

• InfluxDB

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  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• bio_embeddings

  1 434 0.0 HTML

  Get protein embeddings from protein sequences

• evodiff

  1 421 8.9 Python

  Generation of protein sequences and evolutionary alignments via discrete diffusion models

  

Project mention: What’s Next in Protein Design? Microsoft Researchers Introduce EvoDiff: A Groundbreaking AI Framework for Sequence-First Protein Engineering | /r/machinelearningnews | 2023-09-19

Github: https://github.com/microsoft/evodiff

• pypdb

  1 294 5.4 Python

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

• protein-bert-pytorch

  2 137 0.0 Python

  Implementation of ProteinBERT in Pytorch

• DNAnalyzer

  4 123 8.1 Java

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

Project mention: I'm approaching 1000 followers! | dev.to | 2023-06-13

P.S. If you haven't checked out my latest project, DNAnalyzer, please do so! It's a groundbreaking open source tool that brings the power of machine learning to DNA analysis. You can find it on GitHub or read more about it here on dev.to. I would love to hear your feedback and suggestions on how to make it better and more useful for everyone.

• SaaSHub

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• deepblast

  2 99 4.8 Python

  Neural Networks for Protein Sequence Alignment

  

Project mention: [D] To all the machine learning engineers: most difficult model task/type you’ve ever had to work with? | /r/MachineLearning | 2023-07-03

• Peptides

  1 74 2.8 R

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

• pseqsid

  1 11 4.6 Rust

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

protein-sequences related posts

• protr VS seqinr - a user suggested alternative

  2 projects | 5 May 2024

• [D] To all the machine learning engineers: most difficult model task/type you’ve ever had to work with?

  2 projects | /r/MachineLearning | 3 Jul 2023

• protein-bert-pytorch VS provis - a user suggested alternative

  2 projects | 8 Feb 2022

• Please can anyone suggest a good Prot2Vec code?

  1 project | /r/bioinformatics | 12 Oct 2021

• [R] ProteinBERT: A universal deep-learning model of protein sequence and function

  1 project | /r/MachineLearning | 1 Jun 2021

• ProteinBERT: A universal deep-learning model of protein sequence and function

  4 projects | /r/bioinformatics | 30 May 2021
• A note from our sponsor - InfluxDB
  www.influxdata.com | 6 May 2024

  Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality. Learn more →

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