PSTk-Classifier – Classify DNA using a Bayesian approach

PSTk-Classifier

:: DESCRIPTION

PSTk-Classifier is a software written in C++ for classifying DNA using a Bayesian approach. Different underlying models can be selected — Naive (Nk), Markov (Mk) and Variable Length Markov (VLMK). The classifier works by first constructing profiles for all groups using fasta-files directly. The profiles are kept in a directory. Then sample sequences (in a multifasta file) can be scored against the profiles and a high-score list will be presented.

::DEVELOPER

Daniel Dalevi (daniel.dalevi@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PSTk-Classifier

:: MORE INFORMATION

Citation

Dalevi D, Dubhashi D, Hermansson M (2006)
Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.
Bioinformatics. 2006 Mar 1;22(5):517-22.

nuScore – DNA Deformation Energy and Nucleosome-positioning Score Calculator

nuScore

:: DESCRIPTION

nuScore allows estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. The algorithm is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.
nuScore: a web-interface for nucleosome positioning predictions.
Bioinformatics. 2008. 24:1456-1458.

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 – Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models

 BioSeq-Analysis 2.0 / BioSeq-BLM 1.0

:: DESCRIPTION

BioSeq-Analysis is an platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

BioSeq-BLM is a platform for analyzing DNA, RNA, and protein sequences based on biological language models

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

BioSeq-Analysis / BioSeq-BLM

:: MORE INFORMATION

Citation

Li HL, Pang YH, Liu B.
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models.
Nucleic Acids Res. 2021 Sep 28:gkab829. doi: 10.1093/nar/gkab829. Epub ahead of print. PMID: 34581805.

Liu B, Gao X, Zhang H.
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches.
Nucleic Acids Res. 2019 Nov 18;47(20):e127. doi: 10.1093/nar/gkz740. PMID: 31504851; PMCID: PMC6847461.

HDOCK 1.1 – Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy

HDOCK 1.1

:: DESCRIPTION

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HDOCK 

:: MORE INFORMATION

Citation:

Yan Y, Zhang D, Zhou P, Li B, Huang SY.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373. doi: 10.1093/nar/gkx407. PMID: 28521030; PMCID: PMC5793843.

Gelapp 1.2.7 – DNA & Prot Gel Analyzer

Gelapp 1.2.7

:: DESCRIPTION

Gelapp is an app that allows you to analyze gel (both agarose and PAGE) bands with a log graph automatically generated from the markers. It allows automatic detection and loading for future uses. Utilizing Gabor filter, this app allows users to improve detection of bands automatically. For poor quality images, users can click can manually draw a box on the desired band or click on the image to determine the specified location.

::DEVELOPER

Antibody & Product Development Team of BII-p53Lab ASTAR

:: SCREENSHOTS

:: REQUIREMENTS

  • iOS / Android

:: DOWNLOAD

Gelapp for iOS / for Android.

:: MORE INFORMATION

Citation

Nguyen PV, Ghezal A, Hsueh YC, Boudier T, Gan SK, Lee HK.
Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.
Electrophoresis. 2016 Aug;37(15-16):2208-16. doi: 10.1002/elps.201600197. Epub 2016 Jul 4. PMID: 27251892.

DBRandomizer – Randomizes DNA and protein databases

DBRandomizer

:: DESCRIPTION

DBRandomizer randomizes DNA and protein databases in different ways(Markov Chain DB, Shuffle DB, Reverse DB).

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/MacOsX
  • Perl

:: DOWNLOAD

 DBRandomizer

:: MORE INFORMATION

iRO-3wPseKNC / iRO-PsekGCC- Identify DNA Replication Origins

iRO-3wPseKNC / iRO-PsekGCC

:: DESCRIPTION

iRO-3wPseKNC is a webserver of identify DNA replication origins by three-window-based PseKNC

iRO-PsekGCC is a web server to identify DNA replication origins based on Pseudo k-tuple GC Composition

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Liu B, Weng F, Huang DS, Chou KC.
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC.
Bioinformatics. 2018 Sep 15;34(18):3086-3093. doi: 10.1093/bioinformatics/bty312. PMID: 29684124.

Liu B, Chen S, Yan K, Weng F.
iRO-PsekGCC: Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition.
Front Genet. 2019 Sep 18;10:842. doi: 10.3389/fgene.2019.00842. PMID: 31620165; PMCID: PMC6759546.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.

POY 5.1.1 – Phylogenetic Analysis of DNA and other data using Dynamic Homology

POY 5.1.1

:: DESCRIPTION

POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood). A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.

::DEVELOPER

Systematic Biology divisions of the AMNH

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX/ Windows / Linux

:: DOWNLOAD

 POY

:: MORE INFORMATION

Citation

Varón, A., L. S. Vinh, W. C. Wheeler. 2010.
POY version 4: phylogenetic analysis using dynamic homologies.
Cladistics, 26:72-85.

DNABind – DNA Binding Residue Prediction

DNABind

:: DESCRIPTION

DNABind is a novel hybrid algorithm for identifying these crucial residues by exploiting the complementarity between machine learning- and template-based methods.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2013 Nov;81(11):1885-99. doi: 10.1002/prot.24330. Epub 2013 Aug 16.
DNABind: a hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.
Liu R1, Hu J.

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