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PMID: 10592251 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Transterm: a database of messenger RNA components and signals.

Nucleic acids research ·Vol. 28 ·No. 1 ·2000-01-01 ·Pages 293-5

Jacobs GH, Stockwell PA, Schrieber MJ, Tate WP, Brown CM

Abstract

Transterm facilitates studies of messenger RNAs and translational control signals. Each messenger RNA (mRNA) from GenBank is extracted and broken into its functional components, its coding sequence, initiation context, termination context, flanking sequence representing its 5' UTR (untranslated region), 3' UTR and translational signals. In addition, numerical parameters characterising each coding region in Transterm, including codon and GC bias, are available. For each species in Transterm, the initiation and termination regions are aligned by their start or stop codons and presented as base frequency matrices and tables of the information content of the bases in the alignments. Users can obtain summaries of characteristics of the mRNAs for species of their choice and search for translational signals both in the Transterm database and in their own sequence. The current release contains data from over 10 000 species, including the complete genomes of 20 prokaryotes and three eukaryotes. Both flat-file and relational database forms of Transterm are accessible via the WWW at http://biochem.otago.ac.nz/Transterm/

MeSH Terms

Codon, Initiator Codon, Terminator Databases, Factual Information Storage and Retrieval Internet RNA, Messenger/chemistry,genetics

Chemicals

Codon, Initiator Codon, Terminator RNA, Messenger

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Jacobs G H

Department of Biochemistry, University of Otago, Dunedin, New Zealand.

Stockwell P A

Schrieber M J

Tate W P

Brown C M

References (12)

12 references, click to expand

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/28.1.293

Published

2000-01-01

Pages

293-5

Language

English

Region

England

NLM ID

0411011

PMCID

PMC102492

Subset

External Links

PubMed source DOI: 10.1093/nar/28.1.293 PMC Full Text View journal details

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