N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

HBN – Integration of Relational and Hierarchical Network Information for Protein Function Prediction

HBN

:: DESCRIPTION

HBN is a software of hierarchical binomial neighborhood (HBN) method for Protein Function Prediction

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 HBN

:: MORE INFORMATION

Citation

Jiang, X., Nariai, N., Steffen, M., Kasif, S., and Kolaczyk, E.D. (2007).
Integration of Relational and Hierarchical Network Information for Protein Function Prediction.
BMC Bioinformatics, 9:350.

Meta-All 1.2 – Store and Access Information about Metabolic Pathways

Meta-All 1.2

:: DESCRIPTION

Meta-All is a software that allows to store and access information about metabolic pathways, including reaction kinetics, detailed locations, environmental circumstances and taxonomic information.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Meta-All

:: MORE INFORMATION

Citation

S. Weise, I. Grosse, C. Klukas, D. Koschuetzki, U. Scholz, F. Schreiber and B.H. Junker.
Meta-All: a system for managing metabolic pathway information.
BMC Bioinformatics, 7:e465, 2006.

AlphaPred – Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information

AlphaPred

:: DESCRIPTION

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur H & Raghava GP. (2004).
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
Proteins. 55: 83-90

GammaPred – Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information

GammaPred

:: DESCRIPTION

The GammaPred server predicts the gamma turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure. Two neural networks with a single hidden layer have been used where the first sequence-to-structure network is trained on PSI-BLAST obtained position specific matrices. The filtering has been done by second structure-to-structure network trained on output of first net and PSIPRED predicted secondary structure. The training has been carried out using error backpropagation with a sum of square error function(SSE).

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S. (2003)
A neural network based method for prediction of gamma-turns in proteins from multiple sequence alignment.
Protein Science 12: 923-929.

MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Yan GuoJiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211

Human Genome 1.0.2 – Obtain information about a known Gene

Human Genome 1.0.2

:: DESCRIPTION

The Human Genome App is designed so that a person can obtain information about a known gene or discover relationships between genes and diseases, syndromes or traits.

::DEVELOPER

Florence Haseltine

:: SCREENSHOTS

HumanGenome

:: REQUIREMENTS

  •  iPad

:: DOWNLOAD

 Human Genome

:: MORE INFORMATION

MetaCrop – Browsing and Working with Information from the MetaCrop database

MetaCrop

:: DESCRIPTION

MetaCrop is an Add-on to enable browsing of the content of the handcurated Metacrop database. Users can directly load hand-layouted pathway maps or metabolic network models to use for browsing, pathway exploration, data-mapping and analysis or use them for metabolic modelling. The user can also filter the pathway for species specific information, which will be visually highlighted.

::DEVELOPER

Matthias Klapperstueck and Klaus Hippe.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MetaCrop

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D1173-7. Epub 2011 Nov 15.
MetaCrop 2.0: managing and exploring information about crop plant metabolism.
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S.

MICO – Mutation Information Collector

MICO

:: DESCRIPTION

MICO is a meta-tool for automatically querying and collecting related information from multiple biology/bioinformatics enabled web servers with prediction capabilities.

::DEVELOPER

MICO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2014 Jul 22;10(7):469-71. doi: 10.6026/97320630010469. eCollection 2014.
MICO: A meta-tool for prediction of the effects of non-synonymous mutations.
Lee G1, Chen CF

Uniprot DAT File Parser 1.1.5483 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5483

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION