OrientationChecker 1.0 – Check Orientation of 16S rRNA Gene Sequences

OrientationChecker 1.0

:: DESCRIPTION

OrientationChecker is a simple tool for quickly locating the position of partial sequences within the 16S rRNA gene, and determining (and, if necessary, altering) their orientation, without the need for time-consuming multiple sequence alignments.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

OrientationChecker

:: MORE INFORMATION

Citation

KE Ashelford et al. (2006)
New Screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.
Applied and Environmental Microbiology, 72(9): 5734-5741.

Pintail 1.1 – Analyse 16S rRNA Chimera & Anomalies

Pintail 1.1

:: DESCRIPTION

Pintail is a program for detecting and analysing 16S rRNA chimeras and other anomalies. Pintail is a tool for identifying anomalies, including chimeras, within 16S rDNA sequences. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Pintail

:: MORE INFORMATION

Citation

KE Ashelford et al. (2005)
At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies
Applied and Environmental Microbiology, (12): 7724-7736.

Mallard 1.02 – Screen 16S rRNA Clone Libraries contain Chimeras

Mallard 1.02

:: DESCRIPTION

Mallard is a program for screening 16S rRNA clone libraries, and similar multiple sequence alignments for chimeras and other anomalies.The program is based on the Pintail algorithm which works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Mallard

:: MORE INFORMATION

Citation

KE Ashelford et al. (2006)
New Screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.
Applied and Environmental Microbiology, 72(9): 5734-5741.

DySC 20120601 – Software for Greedy Clustering of 16S rRNA Reads

DySC 20120601

:: DESCRIPTION

DySC is a new tool based on the greedy clustering approach which uses a dynamic seeding strategy. Evaluations based on the normalized mutual information criterion shows that DySC produces higher quality clusters than UCLUST and CD-Hit at a comparable runtime.

::DEVELOPER

Zejun Zheng, Stefan Kramer and Bertil Schmidt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

DySC

:: MORE INFORMATION

Citation

DySC: software for greedy clustering of 16S rRNA reads.
Zheng Z, Kramer S, Schmidt B.
Bioinformatics. 2012 Aug 15;28(16):2182-3. Epub 2012 Jun 23.