V-RevComp 1.1 – Detect and Re-orient Reverse Complementary SSU and LSU rRNA Sequences

V-RevComp 1.1

:: DESCRIPTION

V-RevComp is written in Perl and uses hidden Markov models to detect the conserved loci of rRNA genes in order to determine its orientation. The software supports sequence lengths ranging from full-length down to the short reads that are characteristic of next generation sequencing technologies. This tool is highly efficient in detecting and reorienting reverse complementary ribosomal sequences of almost any length and can additionally be used to detect various sequence anomalies.

::DEVELOPER

Martin Hartmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl
HMMER

:: DOWNLOAD

V-RevComp

:: MORE INFORMATION

Citation:

Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH (2011).
V-RevComp: Automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets.
FEMS Microbiology Letters 319(2): 140-145.

Nilsson RH, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Betrand Y, Alfredsson JF, Larsson KH, Kõljalg, U, Abarenkov K (2011).
A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation.
Mycoscience 52(4): 278-282.

V-Xtractor 2.1 – Extraction of Variable Subregions from SSU or LSU rRNA Sequences

V-Xtractor 2.1

:: DESCRIPTION

V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). This tool extracts phylogenetically comparable regions without prior multiple sequence alignments and improves reliability of the data by confirming basic authenticity of the sequence.

::DEVELOPER

Martin Hartmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl
HMMER

:: DOWNLOAD

V-Xtractor

:: MORE INFORMATION

Citation:

Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH (2010).
V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.
Journal of Microbiological Methods 83(2): 250-253.

Metaxa2 2.2.3 – Identification and Classification of Small Subunit (SSU) rRNA Sequences

Metaxa2 2.2.3

:: DESCRIPTION

Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

Metaxa2

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Mar 2. doi: 10.1111/1755-0998.12399.
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J1, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, Nilsson RH.

Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15.
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH.