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Protocols

ProTISA specifications

Information


Unique identifier OMICS_01871
Name ProTISA
Restrictions to use None
Maintained No

Publication for ProTISA

ProTISA citations

 (4)
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

[…] . 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 SupTISA [] have accumulated (post-processed) predictions from different sources. In ORFcor, orthologous sequences are used to identify and correct inconsistencies in the gene and TIS an […]

library_books

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

2011
BMC Genomics
PMCID: 3160421
PMID: 21749696
DOI: 10.1186/1471-2164-12-361

[…] his study were downloaded from RefSeq in 2010 []. List of the genomes is available at our webpage []. To perform analyses of TIS upstream regions, annotations of TISs were collected from the database ProTISA [] or predicted by TriTISA []. ProTISA collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature (IPT), conse […]

library_books

Genome reannotation of Escherichia coli CFT073 with new insights into virulence

2009
BMC Genomics
PMCID: 2785843
PMID: 19930606
DOI: 10.1186/1471-2164-10-552

[…] FT073. In fact, with an alignment of N-terminal sequences (21 amino acids, 100% identity), this has been implemented as a part of a TIS annotation pipeline previously developed for any genome, namely ProTISA []. To have high quality of gene start annotation, herein we applied the ProTISA pipeline for gene start relocation of the CFT073 genome [].Briefly, TISs of genes are collected from 1) experim […]

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

[…] et needs to be as reliable as possible, and should not be 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/pr […]

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ProTISA institution(s)
State Key Lab for Turbulence and Complex System and Department of Biomedical Engineering, Peking University, Beijing, China

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