Gibbs Motif Sampler 3.2 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences

Gibbs Motif Sampler 3.2

:: DESCRIPTION

The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.

::DEVELOPER

Wadsworth Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows with Cygwin/MacOsX

:: DOWNLOAD

 Gibbs Motif Sampler

:: MORE INFORMATION

Citation

Neuwald AF, Liu JS, and Lawrence CE. (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
Protein Sci 4(8):1618-1632. PubMed: 8520488.

Helical wheel tool – Represent a Protein Sequence as a Helical Wheel diagram

Helical wheel tool

:: DESCRIPTION

Helical wheel tool is a tool that will represent a protein sequence as a helical wheel diagram.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web BRowser with  Flash plugin

:: DOWNLOAD

 NO

:: MORE INFORMATION

RandProt – High-order Markov Random models for Protein Sequences

RandProt

:: DESCRIPTION

RandProt efficiently generates random protein sequences from a high-order Markov model.

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

RandProt

:: MORE INFORMATION

 

Concavity 0.1 – Ligand Binding Site Prediction from Protein Sequence and Structure

Concavity 0.1

:: DESCRIPTION

Concavity predicts ligand-binding sites from structure.

::DEVELOPER

John A. Capra , Thomas Funkhouser , Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Concavity

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA1, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

EFI-EST – Generating Protein Sequence Similarity Networks

EFI-EST

:: DESCRIPTION

EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool  is available without cost for the automated generation of protein sequence similarity networks.

::DEVELOPER

EFI-EST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.
Biochim Biophys Acta. 2015 Apr 18. pii: S1570-9639(15)00112-0. doi: 10.1016/j.bbapap.2015.04.015.

RES – Scan Protein Sequence for its Repeatability

RES

:: DESCRIPTION

The RES (REpeatability Scanner) tool allows you to detect the repeatability of an input sequence. It shows how far from a perfect repeat is a sequence. Results will be automatically generated below the parameter selection.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

dAPE – Annotates Homorepeats (polyX) in Protein Sequence Alignments

dAPE

:: DESCRIPTION

dAPE (dAtabase of Polyx Evolution) helps assessing the evolution of homorepeats and their protein context. It uses by default a weak cutoff (4 out of 6 identical amino acids) to help in the identification of emerging and disappearing homorepeats.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Apr 15;33(8):1221-1223. doi: 10.1093/bioinformatics/btw790.
dAPE: a web server to detect homorepeats and follow their evolution.
Mier P, Andrade-Navarro MA.

orthoFind – Obtain Orthologs and Paralogs of Protein Sequence

orthoFind

:: DESCRIPTION

orthoFind searchs for homologous and orthologous proteins at a genomics level. It allows a quick search given one or more query sequences, and it can search either Swiss-Prot, a collection of reference proteomes, or user datasets. These results are accompanied with a simple functional annotation, including a study of their domain architecture.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2015 Dec 1;10(12):e0143906. doi: 10.1371/journal.pone.0143906.
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins.
Mier P, Andrade-Navarro MA, Pérez-Pulido AJ.

SCANPS 2.3.11 – Protein Sequence Scanning Package

SCANPS 2.3.11

:: DESCRIPTION

SCANPS is a sequence database searching program that implements a range of sensitive algorithms for searching protein sequence databases.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCANPS

:: MORE INFORMATION

Citation:

Thomas P. Walsh1, Caleb Webber, Stephen Searle, Shane S. Sturrock and Geoffrey J. Barton
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Nucl. Acids Res. (2008) 36 (suppl 2): W25-W29.

Optimizer – A web server utility that optimize a DNA or Protein sequence

Optimizer

:: DESCRIPTION

OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Puigbò P., Guzmán E.Romeu A. and Garcia-Vallvé S. 2007
OPTIMIZER: A web server for optimizing the codon usage of DNA sequences.
Nucleic Acids Research, 35:W126-W131.