Tag: NCBI

Genome Workbench 3.7.1 – View & Analyze Sequence Data

Genome Workbench 3.7.1

:: DESCRIPTION

Gbench (NCBI Genome Workbench) is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

::DEVELOPER

Genome Workbench Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Genome Workbench

:: MORE INFORMATION

EntrezAJAX 20100216 – An AJAX Endpoint for NCBI’s Entrez Service

EntrezAJAX 20100216

:: DESCRIPTION

EntrezAJAX provides an interface which returns JSON data from the NCBI Entrez service which can be accessed by a web browser directly.

::DEVELOPER

Nick Loman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python
  • BioPython

:: DOWNLOAD

 EntrezAJAX

:: MORE INFORMATION

Citation

Source Code Biol Med. 2010 Jun 21;5:6. doi: 10.1186/1751-0473-5-6.
EntrezAJAX: direct web browser access to the Entrez Programming Utilities.
Loman NJ1, Pallen MJ.

cddApp 1.1.4 – Integration between Cytoscape and the NCBI Conserved Domain Database

cddApp 1.1.4

:: DESCRIPTION

cddApp is a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD).

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

cddapp

:: REQUIREMENTS

:: DOWNLOAD

 cddApp

:: MORE INFORMATION

Citation:

cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database.
Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.
Bioinformatics. 2014 Sep 10. pii: btu605.

Tbl2KnownGene – Convert NCBI.tbl to UCSC knownGene.txt data file

Tbl2KnownGene

:: DESCRIPTION

Tbl2KnownGene is a wrapper tool that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table.

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Tbl2KnownGene

:: MORE INFORMATION

Citation

Bioinformation. 2014 Aug 30;10(8):544-7. doi: 10.6026/97320630010544. eCollection 2014.
Tbl2KnownGene: A command-line program to convert NCBI.tbl to UCSC knownGene.txt data file.
Bai Y

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

ProMatch – Match Peptide and mRNA Sequences to Entries in NCBI RefSeq

ProMatch

:: DESCRIPTION

ProMatch is a Java-based standalone program to match input parameters such as peptide and mRNA sequences to entries in NCBI Reference Sequence Database (RefSeq). ProMatch helps identify and eliminate ambiguous identifications from proteomic and transcriptomic data.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

ProMatch

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

ProMatch

:: MORE INFORMATION

Citation

Physiol Genomics. 2010 Feb 4;40(3):167-83. doi: 10.1152/physiolgenomics.00148.2009. Epub 2009 Dec 8.
Proteomic profiling of nuclei from native renal inner medullary collecting duct cells using LC-MS/MS.
Tchapyjnikov D1, Li Y, Pisitkun T, Hoffert JD, Yu MJ, Knepper MA.

GEOquery 2.58.0 – Get data from NCBI Gene Expression Omnibus (GEO)

GEOquery 2.58.0

:: DESCRIPTION

GEOquery effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools.

::DEVELOPER

Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOquery

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1846-7.
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.
Davis S, Meltzer PS.

Annokey – Gene-based Search for Key-terms in NCBI Gene Database and Associated PubMed Abstracts

Annokey

:: DESCRIPTION

Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Annokey

:: MORE INFORMATION

GsmPlot – Web Server to visualize Epigenome data in NCBI

GsmPlot

:: DESCRIPTION

GsmPlot is a web service to automatically download, analyze and visualize epigenetics data (ChIP-Seq, ATAC-Seq, Bis-Seq), public from NCBI or private from you.

::DEVELOPER

Deqiang Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics, 21 (1), 55 2020 Feb 12
GsmPlot: A Web Server to Visualize Epigenome Data in NCBI
Jia Li , Yue Yin , Mutian Zhang , Jie Cui , Zhenhai Zhang , Zhiyong Zhang , Deqiang Sun