NCBI Influenza Virus Sequence Annotation Tool

NCBI Influenza Virus Sequence Annotation Tool annotates influenza A and B virus nucleotide sequences and predicts the encoded protein sequences for genome annotation and downstream analysis.

Key Features:

• Virus Type and Segment Identification: Uses BLAST to compare input sequences against an influenza sequence database to identify virus type (A or B) and determine segments 1 through 8.
• Subtype Determination for Influenza A: Classifies hemagglutinin (HA) and neuraminidase (NA) segments to determine their subtypes for influenza A viruses.
• Protein Sequence Prediction: Aligns input nucleotide sequences against a curated set of sample protein sequences using ProSplign and uses the translated product of the best alignment as the predicted protein.
• Output Formats: Produces a feature table suitable for GenBank submission via Sequin or tbl2asn, a GenBank flat file, and predicted protein sequences in FASTA format.
• Informative Summary: Generates a summary reporting input sequence length and predictions of virus type, segment, and HA/NA subtype for influenza A.

Scientific Applications:

• Genome annotation: Provides annotated influenza A and B sequences for genomic studies and reference curation.
• Mutation tracking and evolution studies: Enables identification of protein changes to support tracking of mutations and viral evolution analyses.
• Database submission and surveillance: Produces GenBank-compatible outputs to support sequence submission, surveillance efforts, and vaccine-related data sharing.

Methodology:

Compares input sequences to an influenza sequence database using BLAST to identify virus type and segment, then aligns nucleotide sequences to curated sample protein sequences with ProSplign and selects the translated product from the best alignment.