Tag: Clean

CLEAN 1.3.1 – CLustering Enrichment ANalysis

CLEAN  1.3.1

:: DESCRIPTION

 CLEAN is a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score). The score is derived by correlating the clustering structure as a whole with functional categories of interest.

:: DEVELOPER

Laboratory for Statistical Genomics, Univ. Cincinnati

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R Package

:: DOWNLOAD

 CLEAN

:: MORE INFORMATION

Citation:

Freudenberg JM, Joshi VK, Hu Z, Medvedovic M.
CLEAN: CLustering Enrichment ANalysis.
BMC Bioinformatics (2009) 10:234. Pubmed. Poster presented at OCCBIO 2008.

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149

HangOut – Generate Clean PSI-BLAST Profiles for Domains Containing long Insertions

HangOut

:: DESCRIPTION

HangOut is a software for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 HangOut

:: MORE INFORMATION

Citation:

B.H. Kim, Q. Cong, N.V. Grishin (2010)
“HangOut: generating clean PSI-BLAST profiles for domains containing long insertions“.
Bioinformatics (2010) 26 (12): 1564-1565.