Human enterovirus genome annotation

How to annotate EV sequences with VADR

EV VADR model libraries

Additional VADR documentation

References

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How to annotate EV genomes with VADR

Steps for using VADR for EV annotation:

1. Update: requires new version of VADR.

2. Clone the latest EV VADR model library from this repository. git clone git@github.com:greninger-lab/vadr-models-ev.git
   

   Note the path to the directory name created plus the "evA", "evB", "evC", or "evD" subdirectory (e.g. /path/to/vadr-models-ev/evA) as <ev-models-dir-path> for step 4.

3. Remove terminal ambiguous nucleotides from your input fasta sequence file using the fasta-trim-terminal-ambigs.pl script in $VADRSCRIPTSDIR/miniscripts/.

   To remove terminal ambiguous nucleotides from your sequence file <input-fasta-file> and to remove short and long sequences to create a new trimmed file <trimmed-fasta-file>, execute:

$VADRSCRIPTSDIR/miniscripts/fasta-trim-terminal-ambigs.pl --minlen 50 --maxlen 8000 <input-fasta-file> > <trimmed-fasta-file>

4. Run the v-annotate.pl program on an input trimmed fasta file with EV sequences using the recommended command below. In addition, you must indicate the EV species evA, evB, evC or evD as <ev-key>.

v-annotate.pl -r --r_file <ev-models-dir-path>/<ev-key>.rpn.fa --mkey <ev-key> --mdir <ev-models-dir-path> <fasta-file-to-annotate> <output-directory-to-create>

5. After running the v-annotate.pl command in step 4, there will be a number of files generated in the <output-directory-to-create>. Among these files, there are 5-column tab-delimited feature table files that end with the suffix .tbl. There is a separate file for passing (XXXXX.vadr.pass.tbl) and failing (XXXXX.vadr.fail.tbl) sequences. The format of the .tbl files is described here: https://www.ncbi.nlm.nih.gov/genbank/feature_table/

   More information about understanding failures and error alerts can be found in the VADR documentation here: https://github.com/ncbi/vadr/blob/master/documentation/annotate.md

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EV VADR model library

• The VADR model libraries for EV annotation are based on multiple sequence alignments and were developed starting with representative RefSeq sequences and expanding to include one representative from as many ICTV recognized serotypes as possible. This was done iteratively by manually checking annotation and adjusting as necessary. The protein coding region was aligned in protein space and converted to a nucleotide alignment. Structural RNA regions were aligned using Infernal's cmsearch and cmalign programs, and combined with the protein coding region and other non-coding regions, largely manually.

• For evA: sequence MH118079.1 was modified by removing the first 8nt (which were dissimilar from all other model genomes, and so were considered possibly artifactual) and extending the polyA tail from 39 As to 61 As so the model length for the polyA tail could match that of evB, evC and evD.

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Additional VADR documentation

• VADR README
• VADR installation instructions
  • Installation using vadr-install.sh
  • Setting environment variables
  • Verifying successful installation
  • Further information
• v-build.pl example usage and command-line options
  • v-build.pl example usage
  • v-build.pl command-line options
  • Building a VADR model library
  • How the VADR 1.0 model library was constructed
• v-annotate.pl example usage, command-line options and alert information
  • v-annotate.pl example usage
  • v-annotate.pl command-line options
  • Basic Information on v-annotate.pl alerts
  • Additional information on v-annotate.pl alerts
• Explanations and examples of v-annotate.pl detailed alert and error messages
  • Output fields with detailed alert and error messages
  • Explanation of sequence and model coordinate fields in .alt files
  • toy50 toy model used in examples of alert messages
  • Examples of different alert types and corresponding .alt output
  • Posterior probability annotation in VADR output Stockholm alignments
• VADR output file formats
  • VADR output files created by all VADR scripts
  • v-build.pl output files
  • v-annotate.pl output files
  • VADR coords coordinate string format
  • VADR sequence naming conventions

Reference

• The recommended citation for using VADR is: Alejandro A Schäffer, Eneida L Hatcher, Linda Yankie, Lara Shonkwiler, J Rodney Brister, Ilene Karsch-Mizrachi, Eric P Nawrocki; VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics 21, 211 (2020). https://doi.org/10.1186/s12859-020-3537-3

• This page was adapted for EV from Mpox virus annotation

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