English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Predicting the fungal CUG codon translation with Bagheera.

Mühlhausen, S., & Kollmar, M. (2014). Predicting the fungal CUG codon translation with Bagheera. BMC Genomics, 15: 411. doi:10.1186/1471-2164-15-411.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-001A-26D6-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CCB8-C
Genre: Journal Article

Files

show Files
hide Files
:
2049360.pdf (Publisher version), 2MB
Name:
2049360.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show
hide
Description:
-

Creators

show
hide
 Creators:
Mühlhausen, S.1, Author              
Kollmar, M.1, Author              
Affiliations:
1Research Group of Systems Biology of Motor Proteins, MPI for Biophysical Chemistry, Max Planck Society, ou_578570              

Content

show
hide
Free keywords: -
 Abstract: Background: Many eukaryotes have been shown to use alternative schemes to the universal genetic code. While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as leucine, some yeasts, including many but not all of the "Candida", translate the same codon as serine. It has been proposed that the change in codon identity was accomplished by an almost complete loss of the original CUG codons, making the CUG positions within the extant species highly discriminative for the one or other translation scheme. Results: In order to improve the prediction of genes in yeast species by providing the correct CUG decoding scheme we implemented a web server, called Bagheera, that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data. As reference data we use 2071 manually assembled and annotated sequences from 38 cytoskeletal and motor proteins belonging to 79 yeast species. The web service includes a pipeline, which starts with predicting and aligning homologous genes to the reference data. CUG codon positions within the predicted genes are analysed with respect to amino acid similarity and CUG codon conservation in related species. In addition, the tRNA(CAG) gene is predicted in genomic data and compared to known leu-tRNA(CAG) and ser-tRNA(CAG) genes. Bagheera can also be used to evaluate any mRNA and protein sequence data with the codon usage of the respective species. The usage of the system has been demonstrated by analysing six genomes not included in the reference data. Conclusions: Gene prediction and consecutive comparison with reference data from other Saccharomycetes are sufficient to predict the most probable decoding scheme for CUG codons.

Details

show
hide
Language(s): eng - English
 Dates: 2014-05-29
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1186/1471-2164-15-411
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: BMC Genomics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: 10 Volume / Issue: 15 Sequence Number: 411 Start / End Page: - Identifier: -