Transterm: a database to aid the analysis of regulatory sequences in mRNAs - PubMed (original) (raw)

. 2009 Jan;37(Database issue):D72-6.

doi: 10.1093/nar/gkn763. Epub 2008 Nov 4.

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Transterm: a database to aid the analysis of regulatory sequences in mRNAs

Grant H Jacobs et al. Nucleic Acids Res. 2009 Jan.

Abstract

Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3'-untranslated regions (3'-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses.

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Figures

Figure 1.

Figure 1.

Part of the new Transterm user interface. Users select data to analyse from four datasets, e.g. ‘NCBI Genbank—One sequence for each coding sequence entry’. A taxomic group is selected by NCBI ‘TaxId’ number (e.g. 9606), then a particular type of output (listed in Table 1) can be selected by using the pull down menu (e.g. Consensus of initiation region, Figure 2). Data selected can be for all the sequences or a non-redundant set (for H. sapiens 96 417 versus 32 763 sequences). This data can also be searched using Blast or Scan for matches.

Figure 2.

Figure 2.

The ‘Consensus of initiation region’ files for Synechocystis PCC6803 (NBSynePCC_2-1148.initmatrix) and Pseudomonas aeruginosa PAO1 (NBPseuaeru-208964.initmatrix). A count of the percentage of each base in each position is shown (see text for analysis). The position (Pos) in the matrix is shown above −20 to +13, the ATG is at +1 to +3. The consensus (Cons) (>65%) is shown below. For these datasets the upper sequences were 41.7% GC3 and lower 65.8% GC3. More comprehensive descriptions of the data are also available (Table 1).

Figure 3.

Figure 3.

An example of Transterm element description (Puf3p-binding site). Elements may be described by strings, regular expressions, matrices or RNA secondary structure rules. In this case the element is simply described as a string. Users may construct more complex descriptions of the element based on the referenced literature, for example allowing mismatches, insertions or deletions.

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