FLAN: a web server for influenza virus genome annotation

Abstract

FLAN (short for FLu ANnotation), the NCBI web server for genome annotation of influenza virus (http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi) is a tool for user-provided influenza A virus or influenza B virus sequences. It can validate and predict protein sequences encoded by an input flu sequence. The input sequence is BLASTed against a database containing influenza sequences to determine the virus type (A or B), segment (1 through 8) and subtype for the hemagglutinin and neuraminidase segments of influenza A virus. For each segment/subtype of the viruses, a set of sample protein sequences is maintained. The input sequence is then aligned against the corresponding protein set with a ‘Protein to nucleotide alignment tool’ (ProSplign). The translated product from the best alignment to the sample protein sequence is used as the predicted protein encoded by the input sequence. The output can be a feature table that can be used for sequence submission to GenBank (by Sequin or tbl2asn), a GenBank flat file, or the predicted protein sequences in FASTA format. A message showing the length of the input sequence, the predicted virus type, segment and subtype for the hemagglutinin and neuraminidase segments of Influenza A virus will also be displayed.

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

“…Presence or absence of polymorphisms at each locus was encoded as 1 or 0, respectively. The alleles were deduced by linking together the adjacent intervals between the two polymorphic loci and its functionality verified using the National Center for Biotechnology Information FLu ANnotation tool (FLAN; http://www.ncbi.nlm.nih.gov/genomes/FLU/ Database/annotation.cgi) (Bao et al, 2007). Additionally, if the distance that separated two polymorphisms was longer than the length of the reads obtained, then those two polymorphisms were considered not linked.…”

The Avian Influenza Virus NS1 ESEV PDZ Binding Motif Associates with Dlg1 and Scribble To Disrupt Cellular Tight Junctions

“…From 2000 to 2011, NS1 proteins from human influenza A virus isolates generally contain a PBM with the sequence RSKV in H3N2 viruses (ϳ97%) and RSEV in H1N1 viruses (ϳ88%), excluding the 2009 swine origin pandemic H1N1 viruses which encode an NS1 protein with deletion of the PBM. NS1 proteins from H5N1 avian influenza A virus isolates from human infections generally have a PBM with the sequence ESEV (ϳ79% of isolates) (1). The currently circulating highly pathogenic H5N1 influenza viruses generally contain a PBM with the sequence ESEV, with the notable exception of a clade from 1997 H5N1 viruses, where NS1 proteins typically had a noncanonical EPEV PBM (40).…”

“…The currently circulating highly pathogenic H5N1 influenza viruses generally contain a PBM with the sequence ESEV, with the notable exception of a clade from 1997 H5N1 viruses, where NS1 proteins typically had a noncanonical EPEV PBM (40). Since 2000, this subset of NS1 proteins containing the EPEV PBM has become relatively rare in the H5N1 NS1, representing less than 3% of avian origin and less than 1.5% human origin H5N1 NS1 PBMs (1). The human and avian PBM sequences RSKV, RSEV, and ESEV are a canonical class I PBM with the consensus sequence -X-S/T-X-V COOH and are predicted to bind several PDZ proteins (39,40,45,55).…”

Improvisation in evolution of genes and genomes: whose structure is it anyway?

“…In line with this view, while viral genomes are a simple system to study evolution and selection, they are also extremely varied [66] [67]. The variability in viral genomes represents a significant technical challenge for evolutionary comparative genomics.…”