1 Accessing Geptop

1.1 Webserver

Geptop is maintained by CEFG group and for the current is available online at http://gepa.org.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.

• Linux or Windows environment --- Geptop has been tested on Ubuntu and Windows
• Python version 2.x --- The latest version of Python can be obtained from http://www.python.org/
• Biopython library for python 2.x--- Biopython can be obtained from http://biopython.org/
• Standalone NCBI BLAST --- BLAST can be obtained from the NCBI FTP site at ftp://ftp.ncbi.nih.gov/blast/executable

2 Submitting genomes Sequence on the Webserver

The sequence can be submitted at http://gepa.org.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