Annogene: Restful Web Service for Annotating Genomic Features

• Autorzy: Tomski A. , Piechota M. , Przewłocki R.

Identyfikatory

DOI

10.1515/jacsm-2015-0002

• Języki publikacji: EN

Abstrakty

EN

Modern high-throughput sequencing techniques generate a constantly increasing amount of genomic data from eukaryotes. The main problem is quickly identifying the data that may provide information about the nature of intracellular processes, such as the targeting of transcription factor-binding sites. Typically, thousands of peaks or signals are found across the genome and the nearby genes must be annotated. We introduce AnnoGene - a web service for annotating genomic features. AnnoGene was implemented in a representational state transfer (REST) architectural style. The program searches for the gene nearest to the center of a genomic position. Subsequently, the location and annotationsof the gene are shown. The tool can be downloaded and run on a local computer, but it was designed to be a web service. AnnoGene is freely available through a web browser. Moreover, our paper covers examples of the REST clients written in the Python, R and Java programming languages. AnnoGene only requires genomic positions from the user. Even when annotating several thousand positions, the output is typically ready in a few seconds. Moreover, this tool supports Seqinspector – a web tool for finding regulators of the genes.

Słowa kluczowe

EN

BED annotation; RESTful web service; ChIP-seq peaks

• Wydawca: Społeczna Akademia Nauk w Łodzi
• Czasopismo: Journal of Applied Computer Science Methods
• Rocznik: 2014
• Tom: Vol. 6 No. 2
• Strony: 101--110
• Opis fizyczny: Bibliogr. 21 poz., tab.

Twórcy

autor

Tomski A.

• Institute of Mathematics, Jagiellonian University, Kraków, Poland
• Department of Molecular Neuropharmacology, Institute of Pharmacology of the Polish Academy of Sciences, Kraków, Poland

autor

Piechota M.

• Department of Molecular Neuropharmacology, Institute of Pharmacology of the Polish Academy of Sciences, Kraków, Poland

autor

Przewłocki R.

• Department of Molecular Neuropharmacology, Institute of Pharmacology of the Polish Academy of Sciences, Kraków, Poland

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