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ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes.

Hua ZG, Lin Y, Yuan YZ, Yang DC, Wei W, Guo FB - Nucleic Acids Res. (2015)

Bottom Line: Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version.Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it.We hope ZCURVE 3.0 will receive wide use with the web-based running mode.

View Article: PubMed Central - PubMed

Affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.

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Submission interface (left top panel), option menu (left bottom panel), and an example of output information (right panel) using the Portiera aleyrodidarum genome.
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Figure 1: Submission interface (left top panel), option menu (left bottom panel), and an example of output information (right panel) using the Portiera aleyrodidarum genome.

Mentions: For the input, we provide an example of the Portiera aleyrodidarum TV (NC_020831) genome on our ZCURVE web server, which has a very small genome size that enables a quick loading time. When annotating one anonymous genome, the users must prepare a standard FASTA sequence file as well as the example. Also, our server can handle multiple FASTA-formatted sequences, which is especially useful when users submit contigs of a draft genome. Our program can output four files by selecting each of the four output options. One is the chromosomal coordinates of all predicted genes. The second file includes DNA sequences of all genes in FASTA format. The third file corresponds to amino acid sequences encoded by each predicted gene. The last output file contains the essentiality of all predicted genes provided by our post-processing program Geptop. The essentiality score indicates the importance of the gene function: the higher the essentiality score, the more important the gene function. The first three files are output immediately (usually within several seconds), whereas the essentiality information needs over one hour to output. Therefore, users must record the outputting link and view the results two or three hours later. Figure 1 illustrates the submission interface, option menu, and one example of the output for the coding potential and essentiality prediction.


ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes.

Hua ZG, Lin Y, Yuan YZ, Yang DC, Wei W, Guo FB - Nucleic Acids Res. (2015)

Submission interface (left top panel), option menu (left bottom panel), and an example of output information (right panel) using the Portiera aleyrodidarum genome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489317&req=5

Figure 1: Submission interface (left top panel), option menu (left bottom panel), and an example of output information (right panel) using the Portiera aleyrodidarum genome.
Mentions: For the input, we provide an example of the Portiera aleyrodidarum TV (NC_020831) genome on our ZCURVE web server, which has a very small genome size that enables a quick loading time. When annotating one anonymous genome, the users must prepare a standard FASTA sequence file as well as the example. Also, our server can handle multiple FASTA-formatted sequences, which is especially useful when users submit contigs of a draft genome. Our program can output four files by selecting each of the four output options. One is the chromosomal coordinates of all predicted genes. The second file includes DNA sequences of all genes in FASTA format. The third file corresponds to amino acid sequences encoded by each predicted gene. The last output file contains the essentiality of all predicted genes provided by our post-processing program Geptop. The essentiality score indicates the importance of the gene function: the higher the essentiality score, the more important the gene function. The first three files are output immediately (usually within several seconds), whereas the essentiality information needs over one hour to output. Therefore, users must record the outputting link and view the results two or three hours later. Figure 1 illustrates the submission interface, option menu, and one example of the output for the coding potential and essentiality prediction.

Bottom Line: Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version.Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it.We hope ZCURVE 3.0 will receive wide use with the web-based running mode.

View Article: PubMed Central - PubMed

Affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.

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Related in: MedlinePlus