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cagA/vacA Analysis
This tool can be used to predict the genotype of specific region in 2 virulence genes in H.pylori, EPIYA motif of CagA and (s1/s2) and (m1/m2) motifs of VacA from the genome sequence in FASTA format.
AMR Detection
This tool can be used to determine resistance of H.pylori strains to 2 antibiotics, Clarithromycin and Quinolone base on specific acknowledged mutations in 23s rRNA and gyrA genes in H.pylori from the genome sequence in FASTA format.
Genome Comparative Analysis
RAST
cagA and vacA protein sequence alignment
Basic Local Alignment Search Tool
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Clustal Omega
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
Roary
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.
Snippy
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
Gene Extractor
Gene Extractor can be used extract gene from input genome based on sample gene sequence.
JBrowse
JBrowse is a fast and full-featured genome browser.