String Kernel for comparing protein sequences
-
Updated
Mar 2, 2018 - C++
String Kernel for comparing protein sequences
The goal is to minimize the energy of HP-sequences, represented using 2D HP-Model, using the Monti Carlo Simulations techinque.
An algorithm for solving protein sequence alignment which aims to find optimum matching between two amino acid sequences
FASTA file processor is a CMake Project written in modern C++ and designed to take advantage of the new C++17 standard. It is designed to read and write FASTA files quickly and efficiently, and it can be used as a library or a stand-alone program. The project comes with a set of tests using the Catch2 framework.
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.
Adaptation of the official PyTorch implementation for Transformer Interpretability Beyond Attention Visualization, a novel method to visualize classifications by Transformer based networks [CVPR 2021] to ESM.
from protein alignments to deep learning preparatory.
plotting and summary tools for the protein to genome alignments for genome annotations.
Sequence based PPI prediction algorithm is developed using Xgboost. Around 73,000 positive and negative interacting protein pairs were extracted from Pan’s PPI dataset
Scripts to run benchmarks of BLAST and PLAST on a supercomputer
A console application for the estimation of the primary and secondary structure's elements. Input should be the FASTA-formatted "ss.txt" file generated by PDB database.
CaMELS: In silico prediction of calmodulin binding proteins and their binding sites
Finds sequences of nucleotide triplets, called codons, that specifies which amino acid will be added next during protein synthesis.
An open source and cross platform application to fix, and find problems in protein FASTA sequence files.
Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org
A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.
Leri Analytics delivers bioinformatics services for and solutions to both the academic labs and industries.
Map the peptides to its corresponding protein sequence and locate the modification sites
Code and dataset for paper "Proteasomal cleavage prediction: state-of-the-art and future directions"
Add a description, image, and links to the protein-sequences topic page so that developers can more easily learn about it.
To associate your repository with the protein-sequences topic, visit your repo's landing page and select "manage topics."