Tag: Protein Sequence

dasty 3.0.0.9 – Visualize Protein Sequence Feature Information using DAS

dasty 3.0.0.9

:: DESCRIPTION

Dasty3 is a web client for visualizing protein sequence feature information using DAS. Through the DAS registry the client establishes connections to a DAS reference server to retrieve sequence information and to one or more DAS annotation servers to retrieve feature annotations. It merges the collected data from all these servers and provides the user with a unified, aesthetically pleasing, effective view of the sequence-annotated features. Dasty3 uses AJAX to deliver highly interactive graphical functionality in a web browser by executing multiple asynchronous DAS requests.

::DEVELOPER

dasty team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

dasty

:: MORE INFORMATION

Citation:

Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O’Neill K, Martinez F, Salazar GA, Hermjakob H
(15-Sep-2008) Bioinformatics (Oxford, England), 24 (18) :2119-21

RADAR 1.1.5 – Rapid Automatic Detection and Alignment of Repeats in protein sequences

RADAR 1.1.5

:: DESCRIPTION

RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.

::DEVELOPER

European Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python

:: DOWNLOAD

  RADAR

:: MORE INFORMATION

Citation:

Rapid automatic detection and alignment of repeats in protein sequences. (2000)
Heger A. and Holm L.
Proteins 41(2): 224-237.

mpiCUDA-BLASTP 1.0 – Accelerate BLASTP for Scanning Protein Sequence databases on GPU clusters

mpiCUDA-BLASTP 1.0

:: DESCRIPTION

mpiCUDA-BLASTP is designed to accelerate BLASTP for scanning protein sequence databases on GPU clusters, programmed using CUDA, MPI, and OpenMP programming models.

::DEVELOPER

Liu Weiguo (liuweiguo@ntu.edu.sg).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mpiCUDA-BLASTP

:: MORE INFORMATION

 

CKSAAP-Palm 20100528 – Predict Palmitoylation Sites from Protein Sequences

CKSAAP-Palm 20100528

:: DESCRIPTION

CKSAAP-Palm (composition of k-spaced amino acid pairs ) is a tool for predicting palmitoylation sites based on protein sequence.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  CKSAAP-Palm

:: MORE INFORMATION

Citation

Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.
Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.
Protein Engineering, Design and Selection (2009) 22 (11): 707-712.

2ZIP – Prediction of Leucine Zipper Domain from the Protein Sequence

2ZIP

:: DESCRIPTION

2ZIP predicts Leucine Zippers in your amino acid sequence. A potential Leucine Zipper, a repeat of Leucines and a coiled coil will be annotated.

::DEVELOPER

Erich Bornberg-Bauer , Eric Rivals , Martin Vingron

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Perl

:: DOWNLOAD

 2ZIP

:: MORE INFORMATION

Citation

Erich Bornberg-Bauer, Eric Rivals, Martin Vingron
Computational Approaches to Identify Leucine Zippers
Nucleic Acids Res., 26(11):2740-2746;(1998)

DISpro 1.0 – Prediction of Disordered Regions from Protein Sequences

DISpro 1.0

:: DESCRIPTION

DISpro uses a 1D-RNN to predict the probablity that residues are disorder. The probabilities are also thresholded at probablity .5 to make a hard classification. The input to DISpro is the sequence profile, predicted secondary structure, and predicted relative solvent accesiblity.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  DISpro

:: MORE INFORMATION

Citation:

J. Cheng, M. Sweredoski, & P. Baldi.
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.
Data Mining and Knowledge Discovery, vol. 11, no. 3, pp. 213-222, (2005).

ProteinEvaluator 1.0.0 – Protein Sequence Prediction Evaluator

ProteinEvaluator 1.0.0

:: DESCRIPTION

ProteinEvaluator evaluates predictors using SOV, MCC, Q-Score and State Machine

::DEVELOPER

Kristian Kræmmer Nielsen

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ProteinEvaluator

:: MORE INFORMATION

FANN-GO – Predict Gene Ontology terms for a given protein sequence

FANN-GO

:: DESCRIPTION

FANN-GO is a Matlab software that predicts Gene Ontology terms (Molecular Function and Biological Process) for a given protein sequence.

::DEVELOPER

FANN-GO Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FANN-GO

:: MORE INFORMATION

Citation:

Proteins. 2011 Jul;79(7):2086-96. doi: 10.1002/prot.23029. Epub 2011 Apr 19.
Analysis of protein function and its prediction from amino acid sequence.
Clark WT, Radivojac P.

doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences

doublet 1.0

:: DESCRIPTION

doublet is a modified version of the Smith-Waterman algorithm that incorporates patterns of dipeptide covariation to align protein sequences.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  doublet

:: MORE INFORMATION

Citation:

Gavin A. Price, Gavin E. Crooks, Richard E. Green and Steven E. Brenner
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
Bioinformatics 21 (20): 3824-3831.

CRC64 2006 – Improved 64-bit Cyclic Redundancy Check for Protein Sequences

CRC64 2006

:: DESCRIPTION

CRC64 is the source code for an improved CRC-64 routine for hashing protein sequences. This CRC function has been extensively tested on real sequences and articially generated sequences.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • C Complier

:: DOWNLOAD

 CRC64

:: MORE INFORMATION

Make sure that your compiler/system supports 64-bit integer types