G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool
DNAssist: the integrated editing and analysis of molecular biology sequences in Windows
A pure python lazy BAM parser
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
A fast, accurate and configurable seeding framework for short-read DNA sequence alignment
DNA barcoding analysis pipeline
Parallel-DNA-Sequence-Alignment
A couple of assignments I did for a course in computational (molecular) biology @ University of Warsaw
Rank and filter BLAST DNA sequence matches using probabilities and a heuristic scoring model.
Command-line tool for global protein/DNA sequence alignment using a simplified version of the Needleman-Wunsch algorithm
Import and export .SAM (Sequence Alignment/Map format) files in Mathematica
Guide to download NCBI Bioproject sequencing data and script to generate DNA short read alignment dataset from the data.
The project is based on the paper Sequence Alignment by Cross-Correlation and bridges the gap between the knowledge and an useful implementation.
This is a bunch of programs I created in the 2020 Intermediate Coding For Medicine Course. No Stealing.
An automated cloud-based pipeline for Sanger sequencing QC, read merging, primer trimming, and NCBI BLAST identification via Google Colab.
JavaScript implementation of Needleman-Wunsch algorithm for global alignment, hosted on GitHub Pages!
This is a repo for the algorithms solutions towards the DNA alignment problem. I adopt two ways to solve the problem: dp and Divide n' Conquer
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