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Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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Influenza is an acute, highly communicable viral disease that affects the respiratory tract and is responsible for seasonal epidemics worldwide. Influenza A is the most prevalent type associated with widespread outbreaks and is subtyped based on two surface glycoproteins: hemagglutinin (H) and neuraminidase (N), as in H1N1. These glycoproteins are essential for viral infectivity, transmission, and immune recognition. Transmission occurs primarily through respiratory droplets and contaminated...

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Related Experiment Video

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Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

Published on: June 28, 2013

FLAN: a web server for influenza virus genome annotation.

Yiming Bao¹, Pavel Bolotov, Dmitry Dernovoy

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Nucleic Acids Research

|June 5, 2007

Summary

FLAN is an NCBI web server for annotating influenza virus sequences. It predicts protein sequences and provides data for GenBank submission, aiding influenza research.

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Area of Science:

Virology
Bioinformatics
Genomics

Background:

Influenza virus genome annotation is crucial for tracking viral evolution and pathogenesis.
Accurate annotation facilitates sequence submission to public databases like GenBank.

Purpose of the Study:

To introduce FLAN (FLu ANnotation), an NCBI web server for annotating influenza A and B virus sequences.
To provide a tool for validating and predicting protein sequences from user-submitted flu genomes.

Main Methods:

BLAST searching user sequences against an influenza sequence database to determine virus type, segment, and subtype.
Utilizing the Protein to nucleotide alignment tool (ProSplign) for sequence alignment.
Predicting protein sequences based on the best alignment to reference sequences.

Main Results:

FLAN accurately identifies influenza A or B, segment, and subtype (for HA and NA segments of Influenza A).
The server generates output formats suitable for GenBank submission, including feature tables and FASTA files.
Provides sequence length and predicted viral characteristics for user-submitted sequences.

Conclusions:

FLAN offers a valuable resource for researchers needing to annotate influenza virus sequences.
The tool streamlines the process of preparing sequence data for public repositories.
FLAN enhances the accessibility and usability of influenza genome data.