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TICO specifications

Information


Unique identifier OMICS_09993
Name TICO
Alternative name Translation Initiation site Correction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline TICO

Information


Unique identifier OMICS_09993
Name TICO
Alternative name Translation Initiation site Correction
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline TICO

Publications for Translation Initiation site Correction

TICO citations

 (8)
library_books

A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites

2015
PLoS One
PMCID: 4512697
PMID: 26204119
DOI: 10.1371/journal.pone.0133691

[…] rative genomics; and iii) combining multiple predictions. The related tools commonly start from existing genome annotations or genes identified by the before-mentioned prediction tools. For instance, TICO [] was developed to improve the accuracy of TIS annotation by performing an unsupervised classification of strong-TIS and weak-TIS sequences. Similarly, various resources such as ProTISA [] and S […]

library_books

Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence

2011
PLoS One
PMCID: 3102119
PMID: 21633709
DOI: 10.1371/journal.pone.0020519

[…] cted with a combination of prokaryotic gene prediction programs, namely Glimmer v2.13 , Glimmer v3 and GeneMarkHMM , with the prediction accuracy of the translation initiation site (TIS) improved by TiCo . Automatic genome annotation was performed using an in-house annotation pipeline involving a collection of computational feature prediction tools. Protein function was assigned based on BLASTP s […]

library_books

The Complete Genome and Proteome of Laribacter hongkongensis Reveal Potential Mechanisms for Adaptations to Different Temperatures and Habitats

2009
PLoS Genet
PMCID: 2652115
PMID: 19283063
DOI: 10.1371/journal.pgen.1000416

[…] Gene prediction was performed by Glimmer version 3.02, and results post-processed using TICO for improving predictions of translation initiation sites. Automated annotation of the finished sequence was performed by a modified version of AutoFACT , supplemented by analysis by InterProSca […]

call_split

Genome Sequence of Brucella abortus Vaccine Strain S19 Compared to Virulent Strains Yields Candidate Virulence Genes

2008
PLoS One
PMCID: 2364660
PMID: 18478107
DOI: 10.1371/journal.pone.0002193
call_split See protocol

[…] S19 genome were identified with Glimmer . Genes consisting of fewer than 33 aa were eliminated, and those containing overlaps were manually evaluated. Start sites of each predicted gene were tuned by TiCO . Sequences from the intergenic regions were compared to non-redundant protein databases to identify genes missed by the Glimmer prediction. tRNAs were identified with tRNAscan-SE , while ribosom […]

library_books

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

2008
BMC Microbiol
PMCID: 2396165
PMID: 18454850
DOI: 10.1186/1471-2180-8-72

[…] We used an automated gene annotation pipeline provided by PATRIC [] to predict genes in S. meliloti. This pipeline uses a combination of gene prediction programs, Glimmer [], GeneMark [,], TICO [] and RBSfinder [] to predict genes and compares with genes in RefSeq. A total of 512 new protein-coding genes (with length >90 nt) in the intergenic regions of the genome were predicted through […]

call_split

Computational evaluation of TIS annotation for prokaryotic genomes

2008
BMC Bioinformatics
PMCID: 2362131
PMID: 18366730
DOI: 10.1186/1471-2105-9-160
call_split See protocol

[…] biased towards any database/predictor to be evaluated. We have chosen to use the six most recent TIS databases/predictors, namely, RefSeq [], ProTISA [], EasyGene [,], GeneMarkS [], Glimmer 3 [] and TiCo [], to derive the reference set. For any genome, we obtained the reference TIS set by intersecting the annotations of all six databases/predictors; in order to reduce false positives, genes less […]

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TICO institution(s)
Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen Göttingen, Germany

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