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Literature DB >> 15994191

TICO: a tool for improving predictions of prokaryotic translation initiation sites.

Maike Tech¹, Nico Pfeifer, Burkhard Morgenstern, Peter Meinicke.

Abstract

UNLABELLED: We provide the tool 'TICO' (Translation Initiation site COrrection) for improving the results of conventional gene finders for prokaryotic genomes with regard to exact localization of the translation initiation site (TIS). At the current state TICO provides an interface for direct post processing of the predictions obtained from the widely used program GLIMMER. Our program is based on a clustering algorithm for completely unsupervised scoring of potential TIS locations. AVAILABILITY: Our tool can be freely accessed through a web interface at http://tico.gobics.de/ CONTACT: maike@gobics.de

Mesh：

Substances：
Codon, Initiator

Year: 2005 PMID： 15994191 DOI： 10.1093/bioinformatics/bti563

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

Keyword Cloud
Cited

13 in total

1. Prodigal: prokaryotic gene recognition and translation initiation site identification.

Authors: Doug Hyatt; Gwo-Liang Chen; Philip F Locascio; Miriam L Land; Frank W Larimer; Loren J Hauser
Journal: BMC Bioinformatics Date: 2010-03-08 Impact factor: 3.169

2. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

Authors: Oswald R Crasta; Otto Folkerts; Zhangjun Fei; Shrinivasrao P Mane; Clive Evans; Susan Martino-Catt; Betsy Bricker; GongXin Yu; Lei Du; Bruno W Sobral
Journal: PLoS One Date: 2008-05-14 Impact factor: 3.240

3. Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Authors: I-Hsuan Lin; Tze-Tze Liu; Yu-Ting Teng; Hui-Lun Wu; Yen-Ming Liu; Keh-Ming Wu; Chuan-Hsiung Chang; Ming-Ta Hsu
Journal: PLoS One Date: 2011-05-25 Impact factor: 3.240

4. TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites.

Authors: M Tech; B Morgenstern; P Meinicke
Journal: Nucleic Acids Res Date: 2006-07-01 Impact factor: 16.971

5. PATRIC: the VBI PathoSystems Resource Integration Center.

Authors: E E Snyder; N Kampanya; J Lu; E K Nordberg; H R Karur; M Shukla; J Soneja; Y Tian; T Xue; H Yoo; F Zhang; C Dharmanolla; N V Dongre; J J Gillespie; J Hamelius; M Hance; K I Huntington; D Jukneliene; J Koziski; L Mackasmiel; S P Mane; V Nguyen; A Purkayastha; J Shallom; G Yu; Y Guo; J Gabbard; D Hix; A F Azad; S C Baker; S M Boyle; Y Khudyakov; X J Meng; C Rupprecht; J Vinje; O R Crasta; M J Czar; A Dickerman; J D Eckart; R Kenyon; R Will; J C Setubal; B W S Sobral
Journal: Nucleic Acids Res Date: 2006-11-16 Impact factor: 16.971

6. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

Authors: Patrick C Y Woo; Susanna K P Lau; Herman Tse; Jade L L Teng; Shirly O T Curreem; Alan K L Tsang; Rachel Y Y Fan; Gilman K M Wong; Yi Huang; Nicholas J Loman; Lori A S Snyder; James J Cai; Jian-Dong Huang; William Mak; Mark J Pallen; Si Lok; Kwok-Yung Yuen
Journal: PLoS Genet Date: 2009-03-13 Impact factor: 5.917

TICO: a tool for improving predictions of prokaryotic translation initiation sites.

1. Prodigal: prokaryotic gene recognition and translation initiation site identification.

2. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

3. Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

4. TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites.

5. PATRIC: the VBI PathoSystems Resource Integration Center.

6. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

7. Gene prediction in metagenomic fragments based on the SVM algorithm.

8. An unsupervised classification scheme for improving predictions of prokaryotic TIS.

9. Gene prediction in metagenomic fragments: a large scale machine learning approach.

10. Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.