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. 2011 Jan;39(Database issue):D129-35.
doi: 10.1093/nar/gkq971. Epub 2010 Oct 23.

WebGeSTer DB--a transcription terminator database

Anirban Mitra  1 , Anil K Kesarwani, Debnath Pal, Valakunja Nagaraja
Affiliations

WebGeSTer DB--a transcription terminator database

Anirban Mitra et al. Nucleic Acids Res. 2011 Jan.

Abstract

We present WebGeSTer DB, the largest database of intrinsic transcription terminators (http://pallab.serc.iisc.ernet.in/gester). The database comprises of a million terminators identified in 1060 bacterial genome sequences and 798 plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome. Analysis of the results, both at the whole-genome level and with respect to terminators downstream of specific genes, offers insight into the prevalence of canonical and non-canonical terminators across different phyla. The data in the database reinforce the paradigm that intrinsic termination is a conserved and efficient regulatory mechanism in bacteria. Our database is freely accessible.

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Figures

Figure 1.
Figure 1.
Terminators catalogued in the WebGeSTer DB—(i) L-shaped (canonical terminators): hairpin + 10 bp trail having >3 uridylates, (ii) I-shaped: hairpin + ≤3 uridines in the trail, (iii) U-shaped: >1 hairpin in tandem with an interval of <50 nt in between, (iv) V-shaped: two hairpins’ structure, where the second structure starts immediately at the end of first one and (v) X-shaped: convergent type structures that function as terminators for the convergently transcribed genes on two different strands.
Figure 2.
Figure 2.
GeSTerDB and WebGeSTer interface. The user can refine his search for terminator profiles with one or more of the criteria provided. For e.g. a search for ‘Total ORFs >5000’ and ‘Terminators (lowest ΔG)>2500’ would retrieve all genomes which have more than 5000 genes and also greater than 2500 ‘Best’ terminators.
Figure 3.
Figure 3.
Progressive data accession in WebGeSTer DB. A search initiated at a specific genome can finally lead to details about a terminator downstream of a specific gene.
Figure 4.
Figure 4.
TER-MAP—the high-resolution terminator map and browser. From the genome summary page, the user can navigate to a defined region of the genome or to a specific gene. Terminators are represented as ‘lollipops’ at ends of genes. Clicking on any terminator leads to more information about its computed structure and other parameters.
See this image and copyright information in PMC

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