Answers.Body: <p>you could try to submit your sequences to <a href="http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi" rel="nofollow noreferrer">VFDB: a reference database for bacterial virulence factors</a> ; paper here : <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539962/" rel="nofollow noreferrer">reference paper</a>.</p>
  <p>use the VFanalyzer tool</p>
  <blockquote>
  <p>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.</p>
  </blockquote>
  <blockquote>
  <p>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.</p>
  </blockquote>
  <p>Think you need to convert your FASTQ to FASTA first.</p>
  <p>Other resource is : <a href="https://cge.food.dtu.dk/services/VirulenceFinder/" rel="nofollow noreferrer">VirulenceFinder 2.0</a> or <a href="https://cge.food.dtu.dk/services/PathogenFinder/" rel="nofollow noreferrer">PathogenFinder 1.1</a>;  paper ref : <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7512150/" rel="nofollow noreferrer">In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data</a>, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077302" rel="nofollow noreferrer">PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-16T18:04:02.840Z
Answers.LastActivityDate: 2023-02-16T18:12:27.560Z
Answers.LastEditDate: 2023-02-16T18:12:27.560Z
Answers.UserDisplayName: pippo1980
Body: <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-16T18:28:28.323Z
Comments.Text: If you could kindly try to improve the question unless @pippo1980's answer is helpful. This is not a clear question because you appear to be asking a very specific question for undefined code for a database we don't seem to be aware of, i.e. a NCBI virulence factor database. It's not that it's not solvable - but without further information its really hard, e.g. present an example of the Blast result you want to explore.
Comments.UserDisplayName: M__
Tags: <genomics><blast><bacteria><command-line>
Title: How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?
ThreadText: # How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?
  
  (Asked by: username_0 on 2023-02-16)
  
  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.
  
  **Tags:** genomics, blast, bacteria, command-line
  
  > **Comments:**
  > **username_1**: If you could kindly try to improve the question unless @username_2's answer is helpful. This is not a clear question because you appear to be asking a very specific question for undefined code for a database we don't seem to be aware of, i.e. a NCBI virulence factor database. It's not that it's not solvable - but without further information its really hard, e.g. present an example of the Blast result you want to explore.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2023-02-16. Score: 1
  
  you could try to submit your sequences to [VFDB: a reference database for bacterial virulence factors](http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi) ; paper here : [reference paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539962/).
  
  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](https://cge.food.dtu.dk/services/VirulenceFinder/) or [PathogenFinder 1.1](https://cge.food.dtu.dk/services/PathogenFinder/); paper ref : [In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7512150/), [PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077302)
  
  
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