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IPRStats, Overview

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Encyclopedia of Metagenomics

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Definition

IPRStats is a lightweight platform-independent open-source licensed software package for storing and visualizing metagenomic data annotated by Interproscan. IPRStats is unique in that it provides the user with the same annotation choices offered by the popular open reading frame annotation pipeline, Interproscan. IPRStats can be installed either as a Web server or as a stand-alone software.

Introduction

The functional annotation of open reading frames (ORFs) in metagenomic data is a highly challenging problem. The problem is difficult enough with regular genomic data. When functionally annotating metagenomic data, one is confronted with the additional problems arising from sequence fragmentation, imperfect assemblies, unmitigated sequencing errors, partially identified ORFs, and higher rates of error in ORF calling. One way to overcome these problems is to do away with ORF calling altogether. Instead, assembled metagenomic sequences are translated in six open reading frames....

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Abbreviations

EBI:

European Bioinformatics Institute

GO:

Gene Ontology

IMG/M:

Integrated Microbial Genome/Metagenomics

pHMM:

Profile hidden Markov model

PSSM:

Position-specific scoring matrix

SQL:

Structured Query Language

XML:

Extensible Markup Language

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Author information

Authors and Affiliations

  1. Department of Microbiology, Miami University, 32 Pearson Hall, 700 E. High St., Oxford, OH, 45056, USA

    Iddo Friedberg

Authors
  1. Iddo Friedberg
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Correspondence to Iddo Friedberg .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

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© 2012 Springer Science+Business Media New York

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Friedberg, I. (2012). IPRStats, Overview. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_147-4

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  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_147-4

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

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