KNN-ID – Classifier for Discriminating Thermophilic and Mesophilic Proteins

KNN-ID

:: DESCRIPTION

KNN-ID is a new simple and effective classifier for discriminating thermophilic and mesophilic proteins.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  KNN-ID

:: MORE INFORMATION

Citation

Amino Acids. 2013 Feb;44(2):573-80. doi: 10.1007/s00726-012-1374-z. Epub 2012 Aug 1.
A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins.
Zuo YC, Chen W, Fan GL, Li QZ.

iKNN – Classifier for Non-coding RNA Identification in Organelle Genome level

iKNN

:: DESCRIPTION

According to the concept of the K-nearest neighbor technique, a novel decision-making method, an improved K-nearest neighbor classifier (iKNN) which not only use the information of quantity but also similarity distance, is introduced to recognize ncRNAs from different organelle genomes.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  iKNN

:: MORE INFORMATION

Citation

Using the Chou’s pseudo component to predict the ncRNA locations based on the improved K-nearest neighbor (iKNN) classifier.
In prepared.

Centrifuge 1.0.1-beta – Classifier for Metagenomic Sequences

Centrifuge 1.0.1-beta

:: DESCRIPTION

Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Centrifuge

:: MORE INFORMATION

CAMUR – Classifier with Alternative and MUltiple Rule-based models

CAMUR

:: DESCRIPTION

CAMUR is a new method and software package able to extract multiple, alternative, and equivalent classification models.

::DEVELOPER

DMB (Data Mining Big) Team

:: SCREENSHOTS

CAMUR

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • java

:: DOWNLOAD

 CAMUR

:: MORE INFORMATION

Citation

CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules.
Cestarelli V, Fiscon G, Felici G, Bertolazzi P, Weitschek E.
Bioinformatics. 2015 Oct 30. pii: btv635.

TFAM 1.4 – tRNA Function Classifier

TFAM 1.4

:: DESCRIPTION

TFAM is a BioPerl-based tRNA function classifier that uses sequence profile models to classify the function of unknown query tRNAs.

::DEVELOPER

Ardell Lab @ UC Merced

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
  • BioPerl

:: DOWNLOAD

 TFAM

:: MORE INFORMATION

Citation

TFAM 1.0: an online tRNA function classifier.
Tåquist H H, Cui Y, Ardell DH.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W350-3.

IRcall 1.0.2 / IRclassifier 1.0.2 – Intron Retention Call / Classifier

IRcall 1.0.2 / IRclassifier 1.0.2

:: DESCRIPTION

IRcall is a computational tool for IR event detection from RNA-Seq data.

IRclassifier is a supervised machine learning-based approach for IR event detection from RNA-Seq data.

::DEVELOPER

Bioinformatics Lab,School of Computer Science and Technology, Harbin Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IRcall / IRclassifier

:: MORE INFORMATION

Citation

BMC Genomics. 2015;16 Suppl 2:S9. doi: 10.1186/1471-2164-16-S2-S9. Epub 2015 Jan 21.
IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data.
Bai Y, Ji S, Wang Y.

RDP Classifier 2.11 – Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

RDP Classifier 2.11

:: DESCRIPTION

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment

::DEVELOPER

The Ribosomal Database Project 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • Java

:: DOWNLOAD

 RDP Classifier

:: MORE INFORMATION

Citation

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR.
Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.

regshape v1.0 – DNA Shape-based Classifier for Regulatory Elements(R pkg)

regshape v1.0

:: DESCRIPTION

The regshape R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.

::DEVELOPER

The Ramsey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 regshape

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 30. pii: btv391
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J, Ramsey SA.

iTAK 1.5 – Plant Transcription Factor & Protein Kinase Identifier and Classifier

iTAK 1.5

:: DESCRIPTION

iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).

::DEVELOPER

Fei Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl
  • Bioperl

:: DOWNLOAD

 iTAK

:: MORE INFORMATION

EPPIC 2.1.2 – Evolutionary Protein-Protein Interface Classifier

EPPIC 2.1.2

:: DESCRIPTION

EPPIC aims at classifying the interfaces present in protein crystal structures in order to determine whether they are biologically relevant or not.

::DEVELOPER

EPPIC team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 EPPIC

:: MORE INFORMATION

Citation

Protein interface classification by evolutionary analysis.
Duarte JM, Srebniak A, Schärer MA, Capitani G.
BMC Bioinformatics. 2012 Dec 22;13:334. doi: 10.1186/1471-2105-13-334.