An algorithm for solving protein sequence alignment which aims to find optimum matching between two amino acid sequences
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Updated
Feb 18, 2021 - Java
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.
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.
a protein coding regions annotator that will take the alignment file in the PAF/GFF format and will extract the complete coding regions and prepares them for deep learning.
High-throughput prediction of disordered flexible linker regions in proteins
For viewing, analyzing, and generating figures of protein sequence alignments.
Property Prediction for Intrinsically Disordered Proteins (IDPs) using Language Model
Scripts to run benchmarks of BLAST and PLAST on a supercomputer
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.
It contains some scripts for working with biological sequences. It can translate DNA to proteins, extract specific fragment from alignment.
Adding interpretability features to Facebook AI Research's ESM-IF Inverse Folding Model
Projects developed under the Bioinformatics college chair during the 2020/2021 school year
identify the location of a protein within a cell using only its amino acid sequence
Map the peptides to its corresponding protein sequence and locate the modification sites
Repo for running command line-based HH-suite3 software in Jupyter environment provided via Binder.
Code and dataset for paper "Proteasomal cleavage prediction: state-of-the-art and future directions"
a ruby gem for doing everything that you can do with the protein alignments. You can index all the protein alignments, extract the regions of interest, extract the locus, extract the dimensions.
A collection of projects in bioinformatics.
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