spkTools 1.43.0 – Collection of Functions to Analyze Microarray Spike-in data

spkTools 1.43.0

:: DESCRIPTION

spkTools contains functions that can be used to compare expression measures on different array platforms.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 spkTools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Oct;36(17):e108. doi: 10.1093/nar/gkn430. Epub 2008 Aug 1.
Consolidated strategy for the analysis of microarray spike-in data.
McCall MN, Irizarry RA.

HoloVir 1.0 – Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

HoloVir 1.0

:: DESCRIPTION

HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HoloVir

:: MORE INFORMATION

Citation:

Front Microbiol, 7, 822 2016 Jun 9 eCollection 2016
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Patrick W Laffy et al.

genio 1.0.12 – Genetics Input/Output Functions

genio 1.0.12

:: DESCRIPTION

The genio (GENetics I/O) package provides easy-to-use and efficient readers and writers for formats in genetics research.

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

genio

:: MORE INFORMATION

INGA 2.0-1 – Protein Function Prediction

INGA 2.0-1

:: DESCRIPTION

INGA (Interaction Network GO Annotator) is a web server for the prediction of protein function.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.
Piovesan D, Giollo M, Leonardi E, Ferrari C, Tosatto SC.
Nucleic Acids Res. 2015 May 27. pii: gkv523.

IntFOLD 5.0 – Integrated Protein Structure and Function Prediction Server

IntFOLD 5.0

:: DESCRIPTION

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
McGuffin LJ, Atkins JD, Salehe BR, Shuid AN, Roche DB.
Nucleic Acids Res. 2015 Mar 27. pii: gkv236.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W171-6. doi: 10.1093/nar/gkr184. Epub 2011 Mar 31.
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
Roche DB1, Buenavista MT, Tetchner SJ, McGuffin LJ.

Buenavista, M. T., Roche, D. B., & McGuffin, L. J. (2012)
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.
Bioinformatics, 28, 1851-1857

NTXpred – Prediction of Neurotoxins from their Function and Source

NTXpred

:: DESCRIPTION

The aim of NTXpred is to predict neurotoxins and it source and probable functions from primary amino acid sequences

::DEVELOPER

NTXpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S. and Raghava, G. P. S. (2007)
Prediction of neurotoxins based on their function and source.
In Silico Biology 7, 0025

I-TASSER 5.1 – Protein Structure & Function Predictions

I-TASSER 5.1

:: DESCRIPTION

I-TASSER was ranked best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 I-TASSER

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv342.
I-TASSER server: new development for protein structure and function predictions.
Yang J, Zhang Y

Ambrish Roy, Alper Kucukural, Yang Zhang.
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, vol 5, 725-738 (2010)

NRProF – Protein Function Prediction Based on the Neural Response Algorithm

NRProF

:: DESCRIPTION

 NRProF is a novel automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. The main idea of this algorithm is to define a distance metric that corresponds to the similarity of the subsequences and reflects how the human brain can distinguish between different sequences. We predicted the most similar target protein for a given query protein using the two layered neural response algorithm and thereby assigned the GO term associated with the target sequence to the query sequence. Our method predicted and ranked the actual GO term in the first position out of five with an accuracy of 82%. Results of the 5-fold cross validation and the comparison with PFP server indicate the better performance by our method.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package

:: DOWNLOAD

 NRProF

:: MORE INFORMATION

Citation

Hari Krishna Yalamanchili, Quan-Wu Xiao, and Junwen Wang .
A novel neural response algorithm for protein function prediction
BMC Systems Biology 2012, 6(Suppl 1):S19

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.