Format

Send to

Choose Destination
BMC Bioinformatics. 2017 Feb 22;18(1):121. doi: 10.1186/s12859-017-1494-2.

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.

Author information

1
Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina. gonzalez.sergio@inta.gob.ar.
2
Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK.
3
Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina. rivarola.maximo@inta.gob.ar.
4
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB, Argentina. rivarola.maximo@inta.gob.ar.
5
Instituto de Ingeniería Biomédica, Facultad de Ingeniería, Universidad de Buenos Aires, Buenos Aires, Argentina.
6
Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina.
7
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB, Argentina.
8
Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.
9
Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

Abstract

BACKGROUND:

In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species.

RESULTS:

We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results.

CONCLUSIONS:

ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .

KEYWORDS:

Data integration; De novo transcriptomics; Ontology storage; Web application

PMID:
28222698
PMCID:
PMC5320735
DOI:
10.1186/s12859-017-1494-2
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center