CyNeo4j 1.3 – A Cytoscape app to connect to a Neo4j database

CyNeo4j 1.3

:: DESCRIPTION

CyNeo4j allows users to connect to a Neo4j server to use the server as a storage for large graphs, a calculation platform through plugins in Neo4j or query the graph with Cypher.

::DEVELOPER

CyNeo4j team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
  • Neo4j
:: DOWNLOAD

 CyNeo4j

:: MORE INFORMATION

Citation

cyNeo4j: connecting Neo4j and Cytoscape.
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B.
Bioinformatics. 2015 Aug 12. pii: btv460.

C-HMM 1.0 – Program to Identify Remote Homologues from Protein Sequence Database

C-HMM 1.0

:: DESCRIPTION

C-HMM is a software to detect remote/distant homologues from protein sequence databases. It is based on HMMs(Hidden Markov Models) for identifying the deep evolutionary relationships of protein sequences.

::DEVELOPER

C-HMM team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Java
  • HMMER3

:: DOWNLOAD

 C-HMM

:: MORE INFORMATION

Citation

Rapid and Enhanced Remote Homology Detection by Cascacading Hidden Markov Model Searches in Sequence Space.
Kaushik S, Nair AG, Mutt E, Prasanna H, Sowdhamini R.
Bioinformatics. 2015 Oct 10. pii: btv538.

MetaCrop 2.0 – Browsing and Working with Information from the MetaCrop database

MetaCrop 2.0

:: 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

Chair for Life Science Informatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: 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.

TITINdb – Database of Titin Structure, Sequence, Isoform, Variant and Disease Information

TITINdb

:: DESCRIPTION

TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Laddach A, Gautel M, Fraternali F.
TITINdb-a computational tool to assess titin’s role as a disease gene.
Bioinformatics. 2017 Nov 1;33(21):3482-3485. doi: 10.1093/bioinformatics/btx424. PMID: 29077808; PMCID: PMC5860166.

PDBHighlight 1.1.0 – A RasMol Script database

PDBHighlight 1.1.0

:: DESCRIPTION

The aim of pdbHighlight is to maintain a searchable database of RasMol script files, designed to ‘highlight’ various features of the protein molecules whose structures are available in the Protein Data Bank

::DEVELOPER

PDBHighlight team

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 PDBHighlight

:: MORE INFORMATION

PhenoMeter 1.0 – Metabolome Database Search Tool

PhenoMeter 1.0

:: DESCRIPTION

The PhenoMeter is a metabolome database search tool that uses metabolite response patterns or metabolic phenotypes as queries, searching the MetabolomeExpress metabolomics database for significantly similar phenotypes and ranking them by similarity.

::DEVELOPER

PhenoMeter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links.
Carroll AJ, Zhang P, Whitehead L, Kaines S, Tcherkez G, Badger MR.
Front Bioeng Biotechnol. 2015 Jul 29;3:106. doi: 10.3389/fbioe.2015.00106.

DecoyDatabaseBuilder 1.5.47 – Generation of Decoy Sequences for Amino Acid Databases

DecoyDatabaseBuilder 1.5.47

:: DESCRIPTION

DecoyDatabaseBuilder is a module of the PeakQuant suite, it enables the generation of decoy sequences for amino acid databases.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 DecoyDatabaseBuilder

:: MORE INFORMATION

Citation

Proteomics. 2008 Mar;8(6):1129-37. doi: 10.1002/pmic.200701073.
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.
Reidegeld KA1, Eisenacher M, Kohl M, Chamrad D, Körting G, Blüggel M, Meyer HE, Stephan C.

PiPa – Setup and Maintain a Database for Information on PPI and Biological Pathways

PiPa

:: DESCRIPTION

PiPa is a java-based tool to setup and maintain a database for information on Protein-Protein Interactions and biological Pathways integrated from multiple public databases.

::DEVELOPER

Wissensmanagement in der Bioinformatik

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 PiPa

:: MORE INFORMATION

Citation

Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011).
PiPa: Custom Integration of Protein Interactions and Pathways
GI-Jahrestagung 2011, Workshop “Daten In den Lebenswissenschaften”.

BDBM 1.0.3 – BLAST DataBase Manager

BDBM 1.0.3

:: DESCRIPTION

BDBM provides a graphical user interface that allows you to create high quality sequence datasets using the tools included. Using these tools you can perform several common tasks such as doing BLAST alignments, getting the open reading frames of the sequences in a Fasta file or changing the format of a Fasta file.

::DEVELOPER

The SING research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OsX / Linux
  • Java
  • EMBOSS
  • bedtools
  • NCBI’s BLAST

:: DOWNLOAD

 BDBM

:: MORE INFORMATION