The influenza A virus genome is constituted by 8 separate RNA segments (Figure 1). These segments are frequently exchanged between different viruses by a process known as genetic reassortment. Gene exchange can give rise to viruses with novel antigenic and replicative properties. As a result of progress in sequencing technology and instrumentation, complete sequencing of influenza genomes is now becoming part of the routine analysis and characterization of these viruses. Genetic reassortment can be identified by analyzing the sequences of whole virus genomes. However, current bioinformatics tools are not available to analyze segmented virus genomes. Specialized bioinformatics tools to analyze genetic reassortment are needed to help understand its role in host range, virulence and transmissibility of influenza viruses. This web server was developed to meet the growing need to genotype Influenza A viruses.
FluGenome has two running options.
For each option sequences can be pasted into the window in FASTA format or FASTA files can be uploaded from your computer. For the segment option the FASTA file can contain as many viruses as you would like, but must be the same gene segment. For the genotyping option a FASTA files with the gene segments for a single virus can be uploaded. Please see Sample Data for examples of file formats. The sequences are then compared against the database of segment lineages using our BLAST algorithm. The top BLAST results for a user-submitted query sequence are sorted by identity and coverage, and the best result is used to assign a lineage to the query sequence. If the BLAST hit values are below the thresholds (95% for identity and coverage), a lineage will be assigned with an asterisk (*) indicating the query sequence does not meet criteria and may be from a new lineage. If no data is entered "missing data" will appear in the results.
FluGenome database contains three tables, i.e., Segment, Genome, and Genotype. The Segment table includes around 30,000 records of gene segments, each record with detailed information of strain name, segment, serotype, host, country, year, GenBank accession number, nucleotide sequence, and sequence length. The genome table includes 7889 records of virus genomes, where each entry has information of genotype, accession numbers, and other information associated with the virus. When two or more sequences were available for a gene segment, the longest sequence's accession number was used. The Genotype table has 156 unique genotypes with lineage information of all eight gene segments.