Chimera – Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code

Chimera

:: DESCRIPTION

Chimera is an unsupervised computationally efficient approach for exploiting hidden high dimensional information related to the way gene expression is encoded in the ORF, based solely on the genome of the analysed organism.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 Chimera

:: MORE INFORMATION

Citation

Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code without Prior Knowledge.
Zur H, Tuller T.
Bioinformatics. 2014 Nov 29. pii: btu797.

CATCh v1 – Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

CATCh v1

:: DESCRIPTION

CATCh is an ensemble classifier for chimera detection in 16S rRNA sequencing studies

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CATCh

:: MORE INFORMATION

Citation

Appl Environ Microbiol. 2015 Mar;81(5):1573-84. doi: 10.1128/AEM.02896-14. Epub 2014 Dec 19.
CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.
Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P

ChimeraChecker V1.1 – Chimera Checker for Fungal ITS Region

ChimeraChecker V1.1

:: DESCRIPTION

ChimeraChecker is a blast-based open source software package to examine newly generated fungal internal transcribed spacer (ITS) sequences for the presence of potentially chimeric elements in batch mode.

::DEVELOPER

Henrik Nilsson (henrik dot nilsson at dpes dot gu dot se)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ChimeraChecker

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2010 Nov;10(6):1076-81. doi: 10.1111/j.1755-0998.2010.02850.x.
An open source chimera checker for the fungal ITS region.
Nilsson RH1, Abarenkov K, Veldre V, Nylinder S, DE Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E.

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.