Tag: Annotation

ncFANs v2 – non-coding RNA Function Annotation Server

ncFANs v2

:: DESCRIPTION

ncFANs (non-coding RNA Function Annotation Server) re-annotates microarray data and predict ncRNAs functions of interest to the user/functions of Your Favorite ncRNA (YFN). The ncFANs services presently includes to two organisms and three microarray platforms. This is the first web service for the function annotation of long ncRNAs. We believe it will be an important tool for researchers to further analyze the roles of long ncRNAs in various biological processes.

::DEVELOPER

Qi Liao, Hui Xiao,Institute of Computing Technology,China

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ncFANs

:: MORE INFORMATION

Citation

ncFANs: a web server for functional annotation of long non-coding RNAs Nucl.
Acids Res. (2011) 39 (suppl 2): W118-W124.
Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerb?, Runsheng Chen, Zhongdao Wu, Changning Liu,; Yi Zha

SNAP 2.2 – Identification and Annotation of proxy SNPs using HapMap

SNAP 2.2

:: DESCRIPTION

SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Johnson, A. D., Handsaker, R. E., Pulit, S., Nizzari, M. M., O’Donnell, C. J., de Bakker, P. I. W.
SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap
Bioinformatics, 2008 24(24):2938-2939

V-FAT 1.1 – Automated Finishing, Annotation, and QA tool for Viral Assemblies

V-FAT 1.1

:: DESCRIPTION

V-FAT (Viral Finishing and Annotation Toolkit) is a tool to perform automated computational finishing and annotation of de novo viral assemblies. V-FAT uses reference and read data to order and merge contigs, correct frameshifts, and produce NCBI-ready annotation files. It also performs a set of quality assurance measurements including coverage computation by gene or amplicon and identification of potential consensus errors.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 V-FAT

:: MORE INFORMATION

Citation

Charlebois, P, Yang, X, Newman, RM, Henn, MR, Zody, MC (2012)
V-FAT: a post-assembly pipeline for the finishing and annotation of viral genomes.
Submitted.

PeakAnalyzer 1.4 – Genome-wide Annotation of Chromatin Binding and Modification Loci.

PeakAnalyzer 1.4

:: DESCRIPTION

PeakAnalyzer is a Java GUI application comprising two main utilities:1. PeakAnnotator – for annotating genomic loci ,2. PeaksSplitter – for subdividing broad peaks into individual binding sites

::DEVELOPER

Bertone Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PeakAnalyzer

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Aug 6;11:415.
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.

Jannotatix 0.8 – Sequence and Annotation Viewer

Jannotatix 0.8

:: DESCRIPTION

Jannotatix allows you to run algorithms that create predictions or annotations on a set of sequences. Examples are repeat finders, gene finders, splicing or binding site predictors. The results are returned in a common format and can be filtered, viewed and compared using a graphical interface. The main application at the moment is motif discovery on promotor sequences.

::DEVELOPER

Maximilian Haeussler

:: SCREENSHOTS

Jannotatix

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Java

:: DOWNLOAD

 Jannotatix

:: MORE INFORMATION

svmPRAT 1.0 – svm-Based Protein Residue Annotation Toolkit

svmPRAT 1.0

:: DESCRIPTION

svmPRAT is a general purpose protein residue annotation toolkit to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates annotation problem as a classification or regression problem using support vector machines. The key features of svmPRAT are its ease of use to incorporate any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that allows better capture of signals for certain prediction problems.

::DEVELOPER

Huzefa Rangwala

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  svmPRAT

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Dec 22;10:439.
svmPRAT: SVM-based protein residue annotation toolkit.
Rangwala H, Kauffman C, Karypis G.

Reflect – Automated Annotation of Biochemical Terms in web pages

Reflect

:: DESCRIPTION

Reflect is a free service that tags gene, protein, and small molecule names in any web page within a few seconds. Clicking on a tagged term opens a small popup showing summary information, as shown below. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can used by entering a URL in the field above.

::DEVELOPER

Schneider (Reinhard) Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Firefox / Internet Explorer

:: DOWNLOAD

 Reflect

:: MORE INFORMATION

Citation

Nat Biotechnol. 2009 Jun;27(6):508-10.
Reflect: augmented browsing for the life scientist.
Pafilis E, O’Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R.

OnTheFly 2.0 Beta – Automated Annotation of Biochemical Terms in PDF, Text and Microsoft Office documents

OnTheFly 2.0 Beta

:: DESCRIPTION

OnTheFly is a web-based tool capable of annotating genes proteins and chemicals in commonly used document formats such as PDF, Microsoft Word and Excel, comma-separated values, and plain text files.

::DEVELOPER

Schneider (Reinhard) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Apr 1;25(7):977-8. Epub 2009 Feb 17.
OnTheFly: a tool for automated document-based text annotation, data linking and network generation.
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R.

PMUT – Web-based Tool for the Annotation of Pathological Mutations on Proteins

PMUT

:: DESCRIPTION

PMUT is a web-based tool for the annotation of pathological mutations on proteins. PMUT allows the fast and accurate prediction (~80% success rate in humans) of the pathological character of single point amino acidic mutations based on the use of neural networks. The program also allows the fast scanning of mutational hot spots, which are obtained by three procedures: (1) alanine scanning, (2) massive mutation and (3) genetically accessible mutations.

::DEVELOPER

Molecular Recognition & Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  No, Only Web Service

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Jul 15;21(14):3176-8. Epub 2005 May 6.
PMUT: a web-based tool for the annotation of pathological mutations on proteins.
Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, Orozco M.

MetAnnoGen – Metabolic Network Annotation

MetAnnoGen

:: DESCRIPTION

The MetAnnoGen facilitates the reconstruction of metabolic networks. It is an information system to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses.

::DEVELOPER

Dr. Christoph Gille

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 MetAnnoGen

:: MORE INFORMATION

Citation

Metannogen: annotation of biological reaction networks.
Gille C, Hübner K, Hoppe A, Holzhütter HG.
Bioinformatics. 2011 Oct 1;27(19):2763-4. Epub 2011 Aug 8.