FSDB: a Frameshift Signal Database

Overview

Journal Comput Biol Chem

Publisher Elsevier

Date 2007 Jul 17

PMID 17631420

Citations 10

Authors

Sanghoon Moon

Yanga Byun

Kyungsook Han

Affiliations

Soon will be listed here.

Abstract

Programmed frameshifting is a recoding event in which a ribosome shifts reading frame by one or more nucleotides at a specific mRNA signal between overlapping genes. Programmed frameshifting is involved in the expression of many genes in a wide range of organisms, especially in viruses and bacteria. The mechanism of programmed frameshifting is not fully understood despite many studies, and there are few databases available for detailed information on programmed frameshifting. We have developed a database called FSDB (Frameshift Signal Database), which is a comprehensive compilation of experimentally known or computationally predicted data about programmed ribosomal frameshifting. FSDB provides a graphical view of frameshift signals and the genes using programmed frameshifting for their expression. It also allows the user himself/herself to find programmed frameshift sites in genomic sequences using a program called FSFinder (http://wilab.inha.ac.kr/fsfinder2). We believe FSDB will be a valuable resource for scientists studying programmed ribosomal frameshifting. FSDB is freely accessible at http://wilab.inha.ac.kr/fsdb/.

Citing Articles

PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

McNair K, Salamon P, Edwards R, Segall A BMC Bioinformatics. 2024; 25(1):82.

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Characterization of a Novel Double-Stranded RNA Virus from in New Zealand.

Xu Z, Khalifa M, Frampton R, Smith G, McDougal R, MacDiarmid R Viruses. 2022; 14(2).

PMID: 35215841 PMC: 8878296. DOI: 10.3390/v14020247.

High-throughput interrogation of programmed ribosomal frameshifting in human cells.

Mikl M, Pilpel Y, Segal E Nat Commun. 2020; 11(1):3061.

PMID: 32546731 PMC: 7297798. DOI: 10.1038/s41467-020-16961-8.

RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.

Gupta A, Bansal M Brief Bioinform. 2019; 21(4):1151-1163.

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Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.

Atkins J, Loughran G, Bhatt P, Firth A, Baranov P Nucleic Acids Res. 2016; 44(15):7007-78.

PMID: 27436286 PMC: 5009743. DOI: 10.1093/nar/gkw530.

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