Tag: Functional Annotation

ANNOVAR 20210202 – functional ANNOtation of genetic VARiants

ANNOVAR 20210202

:: DESCRIPTION

ANNOVAR (ANNOtation of genetic VARiants) is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides

::DEVELOPER

ANNOVAR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ANNOVAR

:: MORE INFORMATION

Citation:

Wang K, Li M, Hakonarson H.
ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data
Nucleic Acids Research, 38:e164, 2010

Blast2GO 5.2.5 – Functional Annotation Tool

Blast2GO 5.2.5

:: DESCRIPTION

Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Blast2GO

:: MORE INFORMATION

Citation

A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles.
“Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research“,
Bioinformatics, Vol. 21, September, 2005, pp. 3674-3676.

LncADeep – ab initio lncRNA Identification and Functional Annotation tool

LncADeep

:: DESCRIPTION

LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning.First, LncADeep identifies lncRNAs by integrating sequence intrinsic and homology features based on deep belief networks. Second, LncADeep predicts lncRNA-protein interactions using sequence and structure features based on deep neural networks. Third, since accurate lncRNA-protein interactions can help to infer the functions of lncRNAs.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WebBrowser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Nov 15;34(22):3825-3834. doi: 10.1093/bioinformatics/bty428.
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning.
Yang C, Yang L, Zhou M, Xie H, Zhang C, Wang MD, Zhu H.

AutoFACT 3.4 – An Automatic Functional Annotation and Classification Tool

AutoFACT 3.4

:: DESCRIPTION

AutoFACT is a program that analyses nucleotide and protein sequence data, deriving informative functional descriptions by combinining multiple BLAST reports from a selection of databases. AutoFACT assigns functional information, enzyme clasees, and Gene Ontology terms where possible.

::DEVELOPER

the Burger-Lang Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 AutoFACT

:: MORE INFORMATION

Citation

AutoFACT: an automatic functional annotation and classification tool.
Koski LB, Gray MW, Lang BF, Burger G.
BMC Bioinformatics. 2005 Jun 16;6:151.

SNPs&GO – Predictor of Human Disease-related Mutations in Proteins with Functional Annotations

SNPs&GO

:: DESCRIPTION

 SNPs&GO is a server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R
Functional annotations improve the predictive score of human disease-related mutations in proteins
Hum Mutat 30:1237-1244 (2009)

EASE 2.0 – Functional Annotation tool

EASE 2.0

:: DESCRIPTION

EASE(the Expression Analysis Systematic Explorer), developed by DAVID Bioinformatics team, is a customizable, standalone, Windows(c) desktop software application that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. EASE provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools.

::DEVELOPER

DAVID Bioinformatics team

:: SCREENSHOTS

:: REQUIREMENTS

  •  Windows

:: DOWNLOAD

 EASE

:: MORE INFORMATION

Citation

Douglas A. Hosack, Glynn Dennis Jr., Brad T. Sherman, H. Clifford Lane, Richard A. Lempicki.
Identifying Biological Themes within Lists of Genes with EASE.
Genome Biology 2003 4(6):P4.