Fig. 2

General design and information flow of VAPiD. First the provided sequences are used as queries for a local BLAST search (default) or an online BLASTn search. After results have been returned a reference annotation is downloaded, if a specific reference accession number is given then this reference is downloaded. Next the original FASTA file is aligned with the reference FASTA and the resulting alignment is used to map the reference annotations onto the new FASTA. Then custom code runs through the file and handles RNA editing, ribosomal slippage and splicing. These finalized annotations are then plugged into NCBI’s tbl2asn with the author information and sequin files are generated as well as .gbk files which can be used to manually verify accuracy of new annotations. Quality checked .sqn files can be emailed directly to GenBank