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.

Dintor – Functional Annotation of Genomic and Proteomic data

Dintor

:: DESCRIPTION

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Dintor

:: MORE INFORMATION

Citation

Dintor: functional annotation of genomic and proteomic data.
Weichenberger CX, Blankenburg H, Palermo A, D’Elia Y, K?nig E, Bernstein E, Domingues FS.
BMC Genomics. 2015 Dec 21;16(1):1081. doi: 10.1186/s12864-015-2279-5.

COGNIZER – Functional Annotation of Metagenomic Datasets

COGNIZER

:: DESCRIPTION

COGNIZER is a comprehensive stand-alone framework which is enabled to simultaneously provide COG, KEGG, Pfam, GO and SEED subsystem annotations to individual sequences constituting metagenomic datasets.

::DEVELOPER

COGNIZER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • NCBI BLAST
  • RAPSearch2

:: DOWNLOAD

 COGNIZER

:: MORE INFORMATION

Citation

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.
Bose T, Haque MM, Reddy C, Mande SS.
PLoS One. 2015 Nov 11;10(11):e0142102. doi: 10.1371/journal.pone.0142102.

GenoSkyline 1.2.1 – Tissue-specific Functional Annotation

GenoSkyline 1.2.1

:: DESCRIPTION

GenoSkyline functional annotations is currently available for 9 tissue/cell types. Pre-calculated GS scores for hg19 genome are available for download.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 GenoSkyline

:: MORE INFORMATION

Citation

Lu Q.*, Powles R.*, Wang Q., He B., and Zhao H.
Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. (Submitted)

ANNOVAR 20150414 – functional ANNOtation of genetic VARiants

ANNOVAR 20150414

:: 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

PANNZER – Protein Functional Annotation Server

PANNZER

:: DESCRIPTION

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE), EC numbers and GO classes.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL
  • Blast

:: DOWNLOAD

 PANNZER

:: MORE INFORMATION

Citation

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.
Koskinen P, Törönen P, Nokso-Koivisto J, Holm L.
Bioinformatics. 2015 Jan 8. pii: btu851

Better Bunny 2.2 – Functional Annotation for Rabbit Gene

Better Bunny 2.2

:: DESCRIPTION

Better Bunny is an easy to use tool designed primarily to augment Agilent’s transcriptome-wide rabbit, Oryctolagus cuniculus, gene expression microarray

::DEVELOPER

Dombkowski Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 May 8;13:84. doi: 10.1186/1471-2105-13-84.
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny.
Craig DB, Kannan S, Dombkowski AA.

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

SNPnexus – Functional Annotation of novel and publicly known Genetic Variants

SNPnexus

:: DESCRIPTION

SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders.

::DEVELOPER

Cancer Bioinformatics Group at the Barts Cancer Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W65-70. doi: 10.1093/nar/gks364.
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update).
Dayem Ullah AZ, Lemoine NR, Chelala C.