Tag: Eukaryotic Genome

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

BRAKER v2.1.6 / TSEBRA v1.0.3

:: DESCRIPTION

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

TSEBRA (Transcript Selector for BRAKER) is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BRAKER / TSEBRA

:: MORE INFORMATION

Citation

Gabriel L, Hoff KJ, Brůna T, Borodovsky M, Stanke M.
TSEBRA: transcript selector for BRAKER.
BMC Bioinformatics. 2021 Nov 25;22(1):566. doi: 10.1186/s12859-021-04482-0. PMID: 34823473.

Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M.
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
NAR Genom Bioinform. 2021 Jan 6;3(1):lqaa108. doi: 10.1093/nargab/lqaa108. PMID: 33575650; PMCID: PMC7787252.

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

PClouds 1.0 – Identify Repeat Structure in large Eukaryotic Genomes

PClouds 1.0

:: DESCRIPTION

The (PClouds) P-clouds package is designed to identify repeat structure in large eukaryotic genomes using oligonucleotide counts.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

  PClouds

:: MORE INFORMATION

Citation

W. Gu, T. A. Castoe, D. J. Hedges, M. A. Batzer, and D. D. Pollock,
“Identification of repeat structure in large genomes using repeat probability clouds .”
Anal Biochem. 2008 Sep 1;380(1):77-83. Epub 2008 May 20.

CEGMA 2.5 – Annotate Core Genes in Eukaryotic Genomes

CEGMA 2.5

:: DESCRIPTION

CEGMA (Core Eukaryotic Genes Mapping Approach) is a software for building a highly reliable set of gene annotations in the absence of experimental data.

:DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CEGMA

:: MORE INFORMATION

Citation

Genis Parra, Keith Bradnam and Ian Korf.
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Bioinformatics, 23: 1061-1067 (2007)

SigHunt – Horizontal Gene Transfer Finder optimized for Eukaryotic Genomes

SigHunt

:: DESCRIPTION

SigHunt analyses genomic signature of a DNA sequence and outputs the score DIAS.

::DEVELOPER

Institute of Biostatistics and Analyses, Masaryk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 SigHunt

:: MORE INFORMATION

Citation

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.
Jaron KS, Moravec JC, Martínková N.
Bioinformatics. 2014 Feb 6.

TFM-Explorer 2.0 – Analysing Regulatory Regions in Eukaryotic Genomes

TFM-Explorer 2.0

:: DESCRIPTION

TFM-Explorer (Transcription Factor Matrix Explorer) is a program for analysing regulatory regions in eukaryotic genomes. It takes a set of coregulated gene sequences, and search for locally overrepresented transcription factor biding sites.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Python
  • Numpy

:: DOWNLOAD

 TFM-Explorer

:: MORE INFORMATION

Citation

TFM-Explorer: mining cis-regulatory regions in genomes.
Tonon L, Touzet H, Varré JS.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W286-92. doi: 10.1093/nar/gkq473. Epub 2010 Jun 3.

CASSIS / SMIPS 201511 – Prediction of Secondary Metabolite Gene Clusters in Eukaryotic Genomes

CASSIS / SMIPS 201511

:: DESCRIPTION

CASSIS (cluster assignment by islands of sites) is a tool to predict secondary metabolite (SM) gene clusters around a given anchor (or backbone) gene.

SMIPS (secondary metabolites by InterProScan) is a tool to predict secondary metabolite (SM) anchor genes, also called SM backbone genes, in protein sequences.

::DEVELOPER

CASSIS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Perl

:: DOWNLOAD

 CASSIS / SMIPS

:: MORE INFORMATION

Citation

CASSIS and SMIPS: Promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes.
Wolf T, Shelest V, Nath N, Shelest E.
Bioinformatics. 2015 Dec 9. pii: btv713.