I have performed genomic sequencing using nanopore technology and upon analysing using BLAST in the command line I have identified the presence of E.coli. I was wondering if I can add some code to identify the known virulence genes of E.coli which are on the NCBI BLAST database? Thank you.
you could try to submit your sequences to VFDB: a reference database for bacterial virulence factors ; paper here : reference paper.
use the VFanalyzer tool
VFanalyzer provides an automatic analysis pipeline for a systematic screen of known/potential VFs in given complete/draft bacterial genomes. Users can perform the analysis by one of the publicly available bacterial genomes either from our pre-downloaded genome list (Option 1) or via any valid GenBank accession(s) (Option 2). Or alternatively, users can also analyse any private genome data (raw FASTA sequence, predicted proteins, or annotated GenBank format genome) using Option 3. For query with raw FASTA genome, predicted CDSs will be identified using GLIMMER3 prior to the run of VFanalyzer. Please note that, VFanalyzer only accepts query genomes from the genera of bacterial pathogens with full information in VFDB, and it's designed for complete or nearly complete draft genomes. So you are at your own risk if the query genome are derived from other bacteria or only partially sequenced.
NOTE: Due to connetion issue with NCBI, VFanalyzer can not fetch gbk file using Edirect correctly. Please download the file manually and use option3 to submit your jobs, we will find the other way to fix the problem ASAP.
Think you need to convert your FASTQ to FASTA first.
Other resource is : VirulenceFinder 2.0 or PathogenFinder 1.1; paper ref : In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data, PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data