ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

genome and transcriptome alignment extraction

formatting paf output alignments and plotting the paf alignments stats

stitching coding regions from exon alignments for the protein to genome alignments.

intergenic region analyzer from protein alignments to draft genomes.

compleasm genome coverage analysis using awk

maf alignments from protein to genome alignments using awk

protein alignment gem from alignment to graphs

miniprot protein analyzer

miniprot protein alignment analyzer

Implementation of the Combinatorial Extension (cealign) algorithm to align protein structures

Open-source usearch

Benchmark the performance of sequence alignment workflows

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc

Protein Alignment and Detection Interface

MutFold | Human breast cancer associated mutant protein structure prediction and alignment application

FASTA Alignment search for BsaI and BsmBI restriction sites in the ORF6 protein to verify assertions made by Bruttel, et. al. in "Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2."

For viewing, analyzing, and generating figures of protein sequence alignments.

Protein alignment using gap penalty traceback with the Blosum62 Matrix