G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
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Updated
Oct 20, 2022 - C++
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
This bartender version could handle arbitrary length of barcode
Find and visualize rearrangements in DNA sequences
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
A project to sequence the RNA from actual error prone reads from a PCR process and then to analyze the sequenced protein sequence
This project implements substring search and sequence alignment algorithms for molecular sequences analysis. It includes the Rabin-Karp algorithm for substring search and the Needleman-Wunsch algorithm for sequence alignment. Developed in C++17, the code follows Google Style and includes a Makefile for building and testing the program.
A simple yet powerful sequence clustering tool.
Segmenting DNA sequence into ‘words’,https://arxiv.org/pdf/1202.2518.pdf
Multiple Objective Optimization work for optimizing aptamer binding to new targets done in collaboration with Chris Knight and Josh Knowles
MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors
Challenges of the Advanced Algorithms and Parallel Computing course
High performance tools for analyzing coronavirus genome
An algorithm for finding SNPs of a long read compared to a reference genome
Approximate pattern matching with Counting Filter on q-grams using SSE instructions (CF2)
Archival Compression for hiGh-Throughput sequeNcing data
hierarchical clustering of DNA sequence using upcxx
This is a project for Bioinformatics class. It's about finding mutations using 3th gen sequencing method.
Basic seed-and-extend DNA sequence read aligner
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