EMVC 0.3 – Entropy Minimization over Variable Clusters

EMVC 0.3

:: DESCRIPTION

EMVC filters the annotations for each gene set to minimize a measure of entropy across disjoint gene clusters computed for a range of cluster sizes over multiple bootstrap resampled datasets.

::DEVELOPER

H. Robert Frost <rob.frost at dartmouth.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 EMVC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):1698-706. doi: 10.1093/bioinformatics/btu110. Epub 2014 Feb 25.
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC).
Frost HR, Moore JH.

CLUSTOM-CLOUD 1.0.0 – CLUSTering 16S NGS Sequences by Overlap Minimization

CLUSTOM-CLOUD 1.0.0

:: DESCRIPTION

CLUSTOM-CLOUD that is categorized into hierarchical clustering approach is a program for clustering high-throughput 16S sequences with user-defined thresholds.

::DEVELOPER

CLUSTOM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLUSTOM

:: MORE INFORMATION

Citation

Oh J, Choi CH, Park MK, Kim BK, Hwang K, Lee SH, Hong SG, Nasir A, Cho WS, Kim KM.
CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.
PLoS One. 2016 Mar 8;11(3):e0151064. doi: 10.1371/journal.pone.0151064. PMID: 26954507; PMCID: PMC4783016.

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.
Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.
PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623

Chiron – Protein Energy Minimization server

Chiron

:: DESCRIPTION

Chiron is a server that rapidly minimizes steric clashes in proteins using short discrete molecular dynamics(DMD) simulations.

::DEVELOPER

Ding Lab , Dokholyan Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2011 Jan;79(1):261-70. doi: 10.1002/prot.22879.
Automated minimization of steric clashes in protein structures.
Ramachandran S1, Kota P, Ding F, Dokholyan NV.