ZCURVE protocols

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chevron_left Protein-coding gene prediction Essential gene prediction chevron_right
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ZCURVE specifications

Information


Unique identifier OMICS_08761
Name ZCURVE
Interface Web user interface
Restrictions to use None
Input data Genome sequence (FASTA or multi FASTA format)
Computer skills Basic
Version 3.0
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publications for ZCURVE

ZCURVE in pipelines

 (2)
2017
PMCID: 5446729
PMID: 28549438
DOI: 10.1186/s12985-017-0766-9

[…] representative covs with complete genomes available. the open reading frames (orfs), deduced amino acid sequences, and potential cleavage sites in orf1ab were predicted by orf finder (ncbi) and zcurve_cov 2.0 []. sequence alignment and editing were performed using clustalw (version 2.0), bioedit (version 7.1.9), and geneious (version 5.5.9) [, ]. the spike (s) protein structure […]

2015
PMCID: 4408343
PMID: 25908142
DOI: 10.1128/genomeA.00335-15

[…] the ldmnpv-27 strain has a double-stranded circular 164,108-bp dna genome with an average 57.4% gc content. potential open reading frames (orfs) were identified by using the genemarkhmm () and zcurve_v software packages () and subsequently analyzed manually. putative functions of the orfs were predicted with the help of blast (ncbi) () and blast2go ()., at least 162 orfs of the total 174 […]


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ZCURVE in publications

 (36)
PMCID: 5711816
PMID: 29230204
DOI: 10.3389/fmicb.2017.02331

[…] can get essential gene searched by geptop. moreover, the website stored essential genes in 968 bacterial genomes predicted by geptop. users can browse and download the data for further research ()., zcurve () is a program that predicts genes in bacterial or archaeal genomes. it is developed based on the z-curve theory. its latest version zcurve 3.0 has an embedded geptop program, […]

PMCID: 5691658
PMID: 29065456
DOI: 10.3390/v9100307

[…] were selected for annotation if (a) they did not overlap a larger orf by ≥75 bp, and (b) they were predicted to be protein-encoding by both the fgenesv (http://linux1.softberry.com/berry.phtml) and zcurve_v [] algorithms. sequence similarity for these orfs was also sought for using hhpred []., regions of repeated sequences corresponding to likely homologous repeat (hr) regions were also sought […]

PMCID: 5563517
PMID: 28551853
DOI: 10.1007/s00705-017-3419-9

[…] protein-coding genes were predicted using genemarks v4.32 [], glimmer 3.02 (iterative training) [], prodigal v2.6.3 [], metageneannotator v2008/8/19 [], and zcurve_v (zcurve package 3.0) []. trna genes were predicted using trnascan-se [] (though none were found). again, predictions generated with the different programs were compared, and cdss identified […]

PMCID: 5446729
PMID: 28549438
DOI: 10.1186/s12985-017-0766-9

[…] representative covs with complete genomes available. the open reading frames (orfs), deduced amino acid sequences, and potential cleavage sites in orf1ab were predicted by orf finder (ncbi) and zcurve_cov 2.0 []. sequence alignment and editing were performed using clustalw (version 2.0), bioedit (version 7.1.9), and geneious (version 5.5.9) [, ]. the spike (s) protein structure […]

PMCID: 5289999
PMID: 28217108
DOI: 10.3389/fmicb.2017.00058

[…] homopolymers were resequenced. the final consensus accuracy was 99.9982% for the s. eriocheiris genome., putative protein coding sequences (cdss) were identified by glimmer3 (delcher et al., ) and zcurve 1.0 (guo et al., ). functional annotation of cdss was performed through blastp searches against genbank's non-redundant (nr) protein database, followed by manual inspection. transfer rna genes […]


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ZCURVE institution(s)
Department of Physics, Tianjin University, Tianjin, China

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