GEMBASSY: An EMBOSS associated software package for comprehensive genome analyses

Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from the G-language Genome Analysis Environment and its Representational State Transfer (REST) and SOAP web services. GEMBASSY basically contains wrapper programs of G-language REST/SOAP web services to provide intuitive and easy access to various annotations within complete genome flatfiles, as well as tools for analyzing nucleic composition, calculating codon usage, and visualizing genomic information. For example, analysis methods such as for calculating distance between sequences by genomic signatures and for predicting gene expression levels from codon usage bias are effective in the interpretation of meta-genomic and meta-transcriptomic data. GEMBASSY tools can be used seamlessly with other EMBOSS tools and UNIX command line tools. The source code written in C is available from GitHub (https://github.com/celery-kotone/GEMBASSY/) and the distribution package is freely available from the GEMBASSY web site (http://www.g-language.org/gembassy/).

Original languageEnglish
Article number17
JournalSource Code for Biology and Medicine
Volume8
DOIs
Publication statusPublished - 2013 Aug 29

Fingerprint

Molecular biology
Software packages
Molecular Biology
Software
Genes
Genome
Language
Codon
Web services
Apium graveolens
Genomics
UNIX
Computational Biology
Transcriptome
Documentation
Bioinformatics
Metadata
Interoperability
Gene expression
User interfaces

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Information Systems and Management
  • Health Informatics

Cite this

GEMBASSY : An EMBOSS associated software package for comprehensive genome analyses. / Itaya, Hidetoshi; Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru.

In: Source Code for Biology and Medicine, Vol. 8, 17, 29.08.2013.

Research output: Contribution to journalArticle

@article{ce9a73fc63a54860920da46422bce7bc,
title = "GEMBASSY: An EMBOSS associated software package for comprehensive genome analyses",
abstract = "The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from the G-language Genome Analysis Environment and its Representational State Transfer (REST) and SOAP web services. GEMBASSY basically contains wrapper programs of G-language REST/SOAP web services to provide intuitive and easy access to various annotations within complete genome flatfiles, as well as tools for analyzing nucleic composition, calculating codon usage, and visualizing genomic information. For example, analysis methods such as for calculating distance between sequences by genomic signatures and for predicting gene expression levels from codon usage bias are effective in the interpretation of meta-genomic and meta-transcriptomic data. GEMBASSY tools can be used seamlessly with other EMBOSS tools and UNIX command line tools. The source code written in C is available from GitHub (https://github.com/celery-kotone/GEMBASSY/) and the distribution package is freely available from the GEMBASSY web site (http://www.g-language.org/gembassy/).",
author = "Hidetoshi Itaya and Kazuki Oshita and Kazuharu Arakawa and Masaru Tomita",
year = "2013",
month = "8",
day = "29",
doi = "10.1186/1751-0473-8-17",
language = "English",
volume = "8",
journal = "Source Code for Biology and Medicine",
issn = "1751-0473",
publisher = "BioMed Central",

}

TY - JOUR

T1 - GEMBASSY

T2 - An EMBOSS associated software package for comprehensive genome analyses

AU - Itaya, Hidetoshi

AU - Oshita, Kazuki

AU - Arakawa, Kazuharu

AU - Tomita, Masaru

PY - 2013/8/29

Y1 - 2013/8/29

N2 - The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from the G-language Genome Analysis Environment and its Representational State Transfer (REST) and SOAP web services. GEMBASSY basically contains wrapper programs of G-language REST/SOAP web services to provide intuitive and easy access to various annotations within complete genome flatfiles, as well as tools for analyzing nucleic composition, calculating codon usage, and visualizing genomic information. For example, analysis methods such as for calculating distance between sequences by genomic signatures and for predicting gene expression levels from codon usage bias are effective in the interpretation of meta-genomic and meta-transcriptomic data. GEMBASSY tools can be used seamlessly with other EMBOSS tools and UNIX command line tools. The source code written in C is available from GitHub (https://github.com/celery-kotone/GEMBASSY/) and the distribution package is freely available from the GEMBASSY web site (http://www.g-language.org/gembassy/).

AB - The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from the G-language Genome Analysis Environment and its Representational State Transfer (REST) and SOAP web services. GEMBASSY basically contains wrapper programs of G-language REST/SOAP web services to provide intuitive and easy access to various annotations within complete genome flatfiles, as well as tools for analyzing nucleic composition, calculating codon usage, and visualizing genomic information. For example, analysis methods such as for calculating distance between sequences by genomic signatures and for predicting gene expression levels from codon usage bias are effective in the interpretation of meta-genomic and meta-transcriptomic data. GEMBASSY tools can be used seamlessly with other EMBOSS tools and UNIX command line tools. The source code written in C is available from GitHub (https://github.com/celery-kotone/GEMBASSY/) and the distribution package is freely available from the GEMBASSY web site (http://www.g-language.org/gembassy/).

UR - http://www.scopus.com/inward/record.url?scp=84883514925&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84883514925&partnerID=8YFLogxK

U2 - 10.1186/1751-0473-8-17

DO - 10.1186/1751-0473-8-17

M3 - Article

C2 - 23987304

AN - SCOPUS:84883514925

VL - 8

JO - Source Code for Biology and Medicine

JF - Source Code for Biology and Medicine

SN - 1751-0473

M1 - 17

ER -