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.

Figure 1.

(A) A fragment of ProSplign alignment of query influenza A virus segment 4 (at the top) against a signal peptide (first 16 amino acids of BAA21644, at the bottom). Similarity is too low for BLAST to find a significant hit. Translation in the middle becomes the annotation (see signal peptide on ABM22048). (B) The sample protein AAF99671 is aligned against the query sequence CY019262. ProSplign identified the GT/AG splicing junction. Amino acid threonine spans the splicing site. FLAN passes the coordinates of exons from the alignment to the final annotation.

Figure 2.

A sample output of the FLAN tool. The top part is a feature table showing feature locations (for gene and CDS) and qualifiers (gene and product). The lower part shows the diagnostic information about the sequence annotation.

Figure 3.

A NetSchedule (NS) schema. Client (end user) submits data to CGI at NCBI web server. CGI connects and sends data to the NetCache (NC) server. NC keeps data into blob and returns blob_id back to CGI. CGI connects to the NS server, submits request to execute the job with data from blob_id. NS puts this request in a queue and reports assigned job_id back to CGI. The job is waiting to be executed. WorkerNodes (WN) contacts NS constantly to check jobs in a queue. NS gives WN a job with blob_id of input data to execute. WN takes this blob_id, retrieves input data from NC, and executes the job. When execution is done, WN puts result in new blob2 in NC and gets blob2_id back from NC. WN connects to NS and reports job's execution status and blob2_id of result. NS answers to the status request from CGI with ready status and blob2_id. CGI gets blob2_id, connects to NC and retrieves blob2 with resulting data. Results data is presented to client.