Customprodbj v1.2.0 – Customized Protein Database Construction

Customprodbj v1.2.0

:: DESCRIPTION

Customprodbj is a Java-based tool for customized protein database construction. It can be used to (1) build a customized database based on single VCF file, (2) build a customized database based on multiple VCF files from a sample and (3) build a customized database based on multiple VCF files from multiple samples.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

Customprodbj

:: MORE INFORMATION

Kafeen 2.1.0 – Querying Genetic Variation data from database

Kafeen 2.1.0

:: DESCRIPTION

Kafeen is a quick and easy command-line tool for locally querying genetic variation data from dbNSFP, ESP6500SI, 1000 Genomes, and OtoSCOPE. Its output is configurable and is meant to be tailored to your own local database needs.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Ruby
  • Java

:: DOWNLOAD

 Kafeen 

:: MORE INFORMATION

VISDB – Viral Integration Site DataBase

VISDB

:: DESCRIPTION

VISDB is a manually curated database of viral integration sites in the human genome.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z.
VISDB: a manually curated database of viral integration sites in the human genome.
Nucleic Acids Res. 2020 Jan 8;48(D1):D633-D641. doi: 10.1093/nar/gkz867. PMID: 31598702; PMCID: PMC6943068.

metabosearch – Mass-based Metabolite Identification using multiple databases

metabosearch

:: DESCRIPTION

MetaboSearch performs mass-based metabolite search simultaneously against the four major metabolite databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LipidMaps.

::DEVELOPER

Ressom Lab 

:: SCREENSHOTS

metabosearch

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 metabosearch

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e40096. doi: 10.1371/journal.pone.0040096. Epub 2012 Jun 29.
MetaboSearch: tool for mass-based metabolite identification using multiple databases.
Zhou B1, Wang J, Ressom HW.

IM-TORNADO 2.0.3.2 – Illinois Mayo Taxonomy Operations for RNA Database Operations

IM-TORNADO 2.0.3.2

:: DESCRIPTION

IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.

::DEVELOPER

IM-TORNADO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IM-TORNADO

:: MORE INFORMATION

Citation

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries.
Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N.
PLoS One. 2014 Dec 15;9(12):e114804. doi: 10.1371/journal.pone.0114804. eCollection 2014.

KEGGtranslator 2.5 – Visualizing and Converting the KEGG PATHWAY database to various formats

KEGGtranslator 2.5

:: DESCRIPTION

KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

KEGGtranslator

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

   KEGGtranslator

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.
Wrzodek C, Dräger A, Zell A.

Dover Analyzer 0.1.2 – Overlap and Diversity in Antimicrobial Peptide Database

Dover Analyzer 0.1.2

:: DESCRIPTION

Dover Analyzer is a wizard like application that takes collections of databases annotated in FASTA format and guides the user through a few steps to compute the overlap, diversity and redundant or non-redundant sets of peptide sequences.

::DEVELOPER

Molecular Biosilico Discovery MultiSystem

:: SCREENSHOTS

DoverAnalyzer

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Dover Analyzer

:: MORE INFORMATION

Citation

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.
Aguilera-Mendoza L, Marrero-Ponce Y, Tellez-Ibarra R, Llorente-Quesada MT, Salgado J, Barigye SJ, Liu J.
Bioinformatics. 2015 Mar 29. pii: btv180.

RefSeq 207 – NCBI Reference Sequence Database

RefSeq 207

:: DESCRIPTION

RefSeq (the Reference Sequence) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

::DEVELOPER

NCBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

RefSeq

:: MORE INFORMATION

Citation

NCBI Reference Sequences: current status, policy, and new initiatives.
Pruitt KD, Tatusova T, Klimke W, Maglott DR
Nucleic Acids Res 2009 Jan;37(Database issue):D32-6

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.