click here to Geptop 1.0

Geptop2.0: an update of geptop, a gene essentiality prediction tool for complete-genome based on orthology and phylogeny

Essential genes are absolutely required for the survival of an organism and are considered as the foundation of life. Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).

Based on the first version of geptop, geptop2.0 is mainly updated in reference genomes (from 19 species to 37 species), intelligible scoring method and calculation speed.

How to cite the Geptop: 1. Wei W, Ning LW, Ye YN, Guo FB*. (2013) Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. PLoS One. 8(8): e72343.    2.Wen QF, Liu S, Dong C, Guo HX, Gao YZ, Guo FB* (2019) Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes. Front Microbiol. 10:1236.

 

Essentiality score cutoff:
Email address:

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(The file size is limited to 3MB)

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1 Accessing Geptop

1.1 Webserver

Geptop is maintained by CEFG group and for the current is available online at http://cefg.uestc.cn/geptop/.

1.2 Standalone package

Geptop is also available as a standalone python script to run in a Linux or Windows environment. The file is available at the Download. These modules MUST be installed BEFORE Geptop is used.

2 Submitting genomes Sequence on the Webserver

The sequence can be submitted at http://cefg.uestc.cn/geptop/. The “Upload from file” can be used to analyze your local file. Geptop requires the WHOLE-GENOMIC PROTEIN sequences in FASTA format and the essentiality score cutoff (range:0~1,default: 0.24). This format consists of these parts as follow:

  • A “>” symbol at the beginning of the title line and followed a description
  • The sequence itself at a newline

An example of FASTA format:


>gi|16128009|ref|NP_414556.1| chaperone Hsp40, co-chaperone with DnaK [Escherichia coli str. K-12 substr. MG1655]
MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYG
HAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPT
LEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSK
TLSVKIPAGVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEI
EVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGG
PTGEHNSPRSKSFFDGVKKFFDDLTR

3 Submitting Sequences on the Standalone script

Whole-genomic PROTEIN sequences in FASTA format can also be submited on the standalone Geptop. The usage of command line and optional parameters are described below.

Usage: python geptop2.py –i protein.faa [Optional parameters: –p path of BLAST executable –s essentiality score cutoff –o output file ]

4 Output

Output sample:

#Total 14 genes are submitted
#3 of them are predicted as essential genes
Class(essential gene:1,others:0)            Essentiality Score        Protein
0          0.1358                 gi|78059652|ref|YP_3
1          0.1966                 gi|78059654|ref|YP_3
0          0.0704                 gi|78059649|ref|YP_3
0          0.0704                 gi|78059647|ref|YP_3
0          0.1037                 gi|78059657|ref|YP_3
0          0.0704                 gi|78059650|ref|YP_3
0          0.0358                 gi|78059644|ref|YP_3
1          0.2532                 gi|78059655|ref|YP_3
1          0.1966                 gi|78059656|ref|YP_3

... ...


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Statistic from Jun 26,2019