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ribosort : a program for automated data preparation and exploratory analysis of microbial community fingerprints
Author(s) -
SCALLAN Ú.,
LILIENSIEK A.,
CLIPSON N.,
CONNOLLY J.
Publication year - 2008
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1471-8286.2007.01901.x
Subject(s) - terminal restriction fragment length polymorphism , biology , ribosomal intergenic spacer analysis , computational biology , workflow , software , data mining , restriction fragment length polymorphism , computer science , ribosomal rna , genetics , internal transcribed spacer , polymerase chain reaction , database , gene , programming language
ribosort is a computer package for convenient editing of automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) data. It is designed to eliminate the labourious task of manually classifying community fingerprints in microbial ecology studies. This program automatically assigns detected fragments and their respective relative abundances to appropriate ribotypes. It permits simultaneous sorting of multiple profiles and facilitates direct workflow from TRFLP and ARISA output through to community analyses. ribosort also provides several options to merge repeat profiles of a sample into a single composite profile. By creating a ‘ribotypes by samples’ matrix ready for statistical analyses, use of the package saves time and simplifies the preparation of DNA fingerprint data sets for statistical analysis. In addition, ribosort performs exploratory analysis on the data by creating multidimensional scaling plots that compare the similarity of sample profiles using the statistical software r .