BEACON – Automated tool for Bacterial gEnome Annotation ComparisON

BEACON

:: DESCRIPTION

BEACON is a software tool that compares annotations of a particular genome from different Annotation Methods (AMs). It uses GenBank format as input and derives Extended Annotation (EA) along side listing original annotations from individual AMs.

::DEVELOPER

BEACON team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

 BEACON

:: MORE INFORMATION

Citation

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
Kalkatawi M, Alam I, Bajic VB.
BMC Genomics. 2015 Aug 18;16(1):616. doi: 10.1186/s12864-015-1826-4.

FlaiMapper 3.0.0 – Fragment Location Annotation Identification Mapper

FlaiMapper 3.0.0

:: DESCRIPTION

FlaiMapper is a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).

::DEVELOPER

FlaiMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FlaiMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 22. pii: btu696.
FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data.
Hoogstrate Y, Jenster G, Martens-Uzunova ES

Annocript 1.1.3 – Annotation of Transcriptomes

Annocript 1.1.3

:: DESCRIPTION

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission

::DEVELOPER

frank Musacchia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl

:: DOWNLOAD

 Annocript

:: MORE INFORMATION

Citation:

Annocript: a flexible pipeline for the annotation of transcriptomes also able to identify putative long noncoding RNAs.
Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R.
Bioinformatics. 2015 Feb 19. pii: btv106.

SplicingViewer 1.1.0 – Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data

SplicingViewer 1.1.0

:: DESCRIPTION

SplicingViewer is an integrated tool which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.

::DEVELOPER

SplicingViewer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SplicingViewer

:: MORE INFORMATION

Citation

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.

Jannovar 0.36 – A Java library for Exome Annotation

Jannovar 0.36

:: DESCRIPTION

Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides HGVS-compliant annotations for both for variants affecting coding sequences and splice junctions as well as UTR sequences and non-coding RNA transcripts. Jannovar can also perform family-based pedigree analysis with VCF files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data.

::DEVELOPER

The Computational Biology @ Charité Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Jannovar

:: MORE INFORMATION

Citation

Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.
Jannovar: a java library for exome annotation.
Jäger M1, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.

GPA 1.1.0 – Genetic analysis incorporating Pleiotropy and Annotation

GPA 1.1.0

:: DESCRIPTION

GPA is a statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux/ Windows

:: DOWNLOAD

 GPA

:: MORE INFORMATION

Citation

GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation.
Chung D, Yang C, Li C, Gelernter J, Zhao H.
PLoS Genet. 2014 Nov 13;10(11):e1004787. doi: 10.1371/journal.pgen.1004787.

DeAnnCNV – Detection and Annotation of Copy Number Variations from Whole-exome Sequencing data

DeAnnCNV

:: DESCRIPTION

DeAnnCNV, an online tool, designed for precise Detection and Annotation of Copy Number Variations (CNVs) from whole-exome sequencing (WES) data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data.
Zhang Y, Yu Z, Ban R, Zhang H, Iqbal F, Zhao A, Li A, Shi Q.
Nucleic Acids Res. 2015 May 26. pii: gkv556.

BRAKER v2.1.6 – RNA-seq based Eukaryotic Genome Annotation pipeline

BRAKER v2.1.6

:: DESCRIPTION

BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BRAKER

:: MORE INFORMATION

Citation

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M.
Bioinformatics. 2015 Nov 11. pii: btv661

SpectroGene 1.0 – Genome Annotation using Top-down Mass Spectrometry

SpectroGene 1.0

:: DESCRIPTION

SpectroGene is a tool for top-down protein identification using unannotated bacterial genome.

::DEVELOPER

Mikhail Kolmogorov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SpectroGene

:: MORE INFORMATION

Citation:

SpectroGene: a tool for proteogenomic annotations using top-down spectra.
Kolmogorov M, Liu X, Pevzner PA.
J Proteome Res. 2015 Dec 2.

FamAnn 1.0 – Automated Variant Annotation pipeline to facilitate Target Discovery for Family-based Sequencing Studies

FamAnn 1.0

:: DESCRIPTION

FamAnn is an automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.

::DEVELOPER

McCombie lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Perl

:: DOWNLOAD

 FamAnn

:: MORE INFORMATION

Citation

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR.
Bioinformatics. 2014 Jan 13.