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.

ClipCrop – Detecting Structural Variations using Soft-clipping Information

ClipCrop

:: DESCRIPTION

ClipCrop is a tool for detecting structural variations using soft-clipping information From SAM files.

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  ClipCrop

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S7. doi: 10.1186/1471-2105-12-S14-S7.
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M.

ArrayGene 0.3 – Analysis of Genome Centered Microarray Annotation Information

ArrayGene 0.3

:: DESCRIPTION

ArrayGene is a software package for the annotation of microarrays with gene identifiers. The distinctive feature of ArrayGene is the capability of using genomic position of genes to develop comparisons of gene coverage for specific regions of the genome. It provides the tools to construct and maintain custom databases of genes and microarrays probes. It also provides web forms to query the database and create online reports.

::DEVELOPER

Animal Genomics Laboratory ,Department of Animal Science, UC Davis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • MySQL

:: DOWNLOAD

 ArrayGene

:: MORE INFORMATION

Citation

Verdugo, R. A., and J. F. Medrano. 2006.
Comparison of gene coverage of mouse oligonucleotide microarray platforms.
BMC Genomics 2006, 7:58 (doi:10.1186/1471-2164-7-58

KAGIANA 200906 – Retrieve Information of the Arabidopsis Genes

KAGIANA 200906

:: DESCRIPTION

KAGIANA (Kazusa Arabidopsis Gene Information And Network Analysis) is a macro programs for Microsft Excel facilitating Arabidopsis researchers to retrieve information of the Arabidopsis genes.

::DEVELOPER

Kazusa DNA Research Institute

:: SCREENSHOTS

KAGIANA

:: REQUIREMENTS

  • Windows/ Linux
  • Excel

:: DOWNLOAD

  KAGIANA

:: MORE INFORMATION

Citation

KAGIANA: an Excel-based tool for retrieving summary information on Arabidopsis genes.
Ogata, Y., Sakurai, N., Aoki, K., Suzuki, H., Okazaki, K., Saito, K., Shibata, D.
Plant and Cell Physiology, 50(1):173-177 (2009)

COMSPARI 20031215 – Comparison of Spectral and Retention Information

COMSPARI 20031215

:: DESCRIPTION

COMSPARI (COMparison of SPectral And Retention Information) is a software that has been written to facilitate the analysis of “paired” samples, i.e. samples that are almost identical yet present some qualitative difference. The software was originally written for the analysis of data files produced by GC/MS and LC/MS, but can be used for other techniques, too.

::DEVELOPER

COMSPARI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 COMSPARI

:: MORE INFORMATION

Citation

J Am Soc Mass Spectrom. 2004 Apr;15(4):580-4.
A new technique (COMSPARI) to facilitate the identification of minor compounds in complex mixtures by GC/MS and LC/MS: tools for the visualization of matched datasets.
Katz JE, Dumlao DS, Clarke S, Hau J.

Labmatica 2.2.3 RC1 – Laboratory Information Management System

Labmatica 2.2.3 RC1

:: DESCRIPTION

Labmatica is a Laboratory Information Management System ( LIMS ). With Labmatica you can: manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. Ready made reports and certificates are included in the distribution. You can easily configure these report templates to your corporate identity.

::DEVELOPER

LIMS at work GmbH

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Labmatica

:: MORE INFORMATION

Buy Labmatica LIMS

Multifasta Analysis 0.1 – Get Informations about a set of Contigs

Multifasta Analysis 0.1

:: DESCRIPTION

Multifasta Analysis is used to get informations(N50, max contig, min, amount, amount of bases) about a set of contigs

::DEVELOPER

Prof. Rommel Ramos

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  Multifasta Analysis

:: MORE INFORMATION