:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: 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.
:: DESCRIPTION
TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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”.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION