Contact

Hidetoshi Itaya
   celery [at] g-language.org
Institute for Advanced Biosciences, Keio University
   997-0035 Japan
   Tel/Fax: +81-466-47-5099

GEMBASSY: an EMBOSS associated G-language GAE extension package

Introduction

GEMBASSY is an EMBOSS associated software (EMBASSY) package of 53 tools implemented with methods from G-language GAE. The tools can perform powerful whole genome analyses such as prediction of replication origins and termini, estimation of gene expression from codon usage, and genome information visualization. GEMBASSY is available for installation from source and ready for use through the EMBOSS Explorer interface.

Availability

Quick Start
Get started now via EMBOSS Explorer interface!

Download
The current version is 1.0.3.
GEMBASSY package is released under the GNU General Public License version 2.

Publications

Itaya, H. Oshita, K. Arakawa, K. and Tomita, M. (2013) GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses, Source Code Biol. Med., 6, 9.
Free Full Text PubMed

Source Code

The source code is also freely available from GitHub.

Manuals

The README included in GEMBASSY is available from here.
Original documentation for G-language GAE can be seen here.
The link to the manual entries in EMBOSS Explorer is available in the list of tools below.

Screenshots

Example Workflows

Workflows
Example 1 Example 2
Highslide JS Highslide JS
Example 1: Conservation of Shine-Dalgarno sequence in highly and lowly expressed genes in B. subtilis Example 2: Differences of sequence composition bias of normal and shuffled sequences in B. subtilis
Example 3 Example 4
Highslide JS Highslide JS
Example 3: Analysis of DNA binding domain of operon regulator genes in E. coli Example 4: Examples of applications with graphical output

List of Tools

Name Function References Documentation
gaminoinfo Print out basic amino acid sequence statsitics Lobry and Gautier, 1994
Zavala et al., 2002
Manual (EMBOSS Explorer)
gb1 Calculate strand bias of bacterial genome using B1 index Lobry and Sueoka, 2002
Rocha et al., 2006
Manual (EMBOSS Explorer)
gb2 Calculate strand bias of bacterial genome using B2 index Lobry and Sueoka, 2002
Manual (EMBOSS Explorer)
gbasecounter Create a position weight matrix of oligomers around start codon None Manual (EMBOSS Explorer)
gbaseentropy Calculate and graph the sequence conservation using Shanon uncertainty (entropy) None Manual (EMBOSS Explorer)
gbaseinformationcontent Calculate and graph the sequence conservation using information content None Manual (EMBOSS Explorer)
gbaserelativeentropy Calculate and graph the sequence conservation using Kullback-Leibler divergence (relative entropy) None Manual (EMBOSS Explorer)
gbasezvalue Extract conserved oligomers per position using Z-score None Manual (EMBOSS Explorer)
gbui Calculate base usage indeces for protein-coding sequences None Manual (EMBOSS Explorer)
gcai Calculate codon adaptation index for each gene Sharp and Li, 1987
Manual (EMBOSS Explorer)
gcbi Calculate the codon bias index (CBI) Comeron and Aguade, 1998
Morton, 1993
Manual (EMBOSS Explorer)
gcgr Create a Chaos Game Representation of a given sequence Arakawa et al., 2009
Almeida et al., 2001
Manual (EMBOSS Explorer)
gcircularmap Draw a circular map of the genome None Manual (EMBOSS Explorer)
gcodoncompiler Calculate various kinds of amino acid anc codon usage data Arakawa et al., 2008
Suzuki et al., 2005
Manual (EMBOSS Explorer)
gconsensusz Calculate consensus in given sequences None Manual (EMBOSS Explorer)
gdeltaenc Calculate the codon usage bias related to translation optimization (delta ENC) Rocha, 2004
Manual (EMBOSS Explorer)
gdeltagcskew Calculate the strand bias of bacterial genome using delta GC skew index None Manual (EMBOSS Explorer)
gdinuc Calculate dinucleotide usage Tan et al., 2004
Manual (EMBOSS Explorer)
gdistincc Calculate the distance between two loci in circular chromosomes None Manual (EMBOSS Explorer)
gdnawalk Draw a DNA Walk map of the genome None Manual (EMBOSS Explorer)
genc Calculate the effective number of codons (Nc) Comeron and Aguade, 1998
Wright, 1990
Manual (EMBOSS Explorer)
gentrez Search NCBI Entrez None Manual (EMBOSS Explorer)
genret Retrieves various gene features from genome flatfile None Manual (EMBOSS Explorer)
gew Calculate a measure of synonymous codon usage evenness (Ew) Suzuki et al., 2004
Suzuki et al., 2007
Manual (EMBOSS Explorer)
gfindoriter Predict the replication origin and terminus in bacterial genomes Frank and Lobry, 2000
Arakawa et al., 2007
Manual (EMBOSS Explorer)
gfop Calculate the frequency of optimal codons (Fop) Ikemura, 1981
Ikemura, 1985
Manual (EMBOSS Explorer)
ggcsi GC Skew Index: an index for strand-specific mutational bias Arakawa and Tomita, 2007
Manual (EMBOSS Explorer)
ggcskew Calculate the GC skew of the input sequence None Manual (EMBOSS Explorer)
ggcwin Calculate the GC content along the given genome None Manual (EMBOSS Explorer)
ggeneskew Calculate the gene strand bias of the given genome None Manual (EMBOSS Explorer)
ggenomemap3 Draw a map of the genome None Manual (EMBOSS Explorer)
ggenomicskew Calculate the GC skew in different regions of the given genome None Manual (EMBOSS Explorer)
gicdi Calculate the intrinsic codon deviation index (ICDI) Comeron and Aguade, 1998
Freire-Picos et al., 1994
Manual (EMBOSS Explorer)
gkmertable Create an image showing all k-mer abundance within a sequence Arakawa et al., 2009
Almeida et al., 2001
Manual (EMBOSS Explorer)
gldabias Calculate the strand bias of bacterial genome using linear discriminant analysis (LDA) Rocha et al., 1999
Manual (EMBOSS Explorer)
gnucleotideperiodicity Check the periodicity of certain oligonucleotides None Manual (EMBOSS Explorer)
goligomercounter Count the number of given oligomers in a sequence None Manual (EMBOSS Explorer)
goligomersearch Search oligomers in given sequence None Manual (EMBOSS Explorer)
gp2 Calculate the P2 index of each gene Gouy and Gautier, 1982
Manual (EMBOSS Explorer)
gpalindrome Search palindrome sequences None Manual (EMBOSS Explorer)
gphx Identify predicted highly expressed gene Henry and Sharp, 2007
Karlin and Mrazek, 2000
Manual (EMBOSS Explorer)
gqueryarm Get the replication arm name (left or right) from the given position None Manual (EMBOSS Explorer)
gquerystrand Get the strand name (leading or lagging) from the given position None Manual (EMBOSS Explorer)
greporiter Get the positions of replication origin and terminus Gao and Zhang, 2007
Kono et al., 2011
Frank and Lobry, 2000
Manual (EMBOSS Explorer)
gsvalue Calculate the strength of selected codon usage bias (S) Sharp et al., 2005
Vieira-Silva and Rocha, 2010
Manual (EMBOSS Explorer)
gscs Calculate the scaled chi-square Comeron and Aguade, 1998
Shields and Sharp, 1987
Manual (EMBOSS Explorer)
gseq2png Convert a sequence to PNG image None Manual (EMBOSS Explorer)
gseqinfo Print out basic nucleotide sequence statsitics None Manual (EMBOSS Explorer)
gshuffleseq Create randomized sequence with conserved k-mer composition Fisher and Yates, 1938
Durstenfeld, 1964
Jiang et al., 2008
Kandel et al., 1996
Propp and Wilson, 1998
Manual (EMBOSS Explorer)
gsignature Calculate the oligonucleotide usage (genomic signature) Campbell et al., 1999
Karlin, 2001
Manual (EMBOSS Explorer)
gviewcds Display a graph of nucleotide contents around start and stop codons None Manual (EMBOSS Explorer)
gwvalue Calculate the 'relative adapptiveness of each codon' (W) Sharp et al., 2005
Sakai et al., 2001
Nakamura and Tabata, 1987
Sharp and Li, 1987
Manual (EMBOSS Explorer)
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