xGDBvm – A Cloud-enabled Genome Annotation Platform

xGDBvm

:: DESCRIPTION

xGDBvm is a web-based platform for annotating and visualizing eukaryotic genomes.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux
  • PHP

:: DOWNLOAD

xGDBvm

:: MORE INFORMATION

Citation

Duvick J, Standage DS, Merchant N, Brendel VP.
xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.
Plant Cell. 2016 Apr;28(4):840-54. doi: 10.1105/tpc.15.00933. Epub 2016 Mar 28. PMID: 27020957; PMCID: PMC4863385.

ParsEval 0.9.2 – Compare Two Sets of Gene Structure Annotations

ParsEval 0.9.2

:: DESCRIPTION

ParsEval is a program for comparing two sets of gene structure annotations (provided as GFF3 files) for the same genomic region. Comparison statistics are calculated for each genic region, as well as for the entire region overall.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ParsEval

:: MORE INFORMATION

Citation

Standage, D.S. & Brendel, V.P. (2011)
ParsEval: parallel comparison and analysis of gene structure annotations
BMC Bioinformatics 2012, 13:187

yrGATE 2.0.1 – Gene Structure Annotation Tool

yrGATE 2.0.1

:: DESCRIPTION

yrGATE (Your Gene structure Annotation Tool for Eukaryotes) is a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.yrGATE provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

yrGATE

:: MORE INFORMATION

Citation

Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006)
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.
Genome Biol. 7, R58.

XRNA 2.0 – Creation, Annotation & Display of RNA Secondary Structure Diagrams

XRNA 2.0

:: DESCRIPTION

XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.

::DEVELOPER

RNA Center, UCSC

:: SCREENSHOTS


:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Perl

:: DOWNLOAD

XRNA

:: MORE INFORMATION

STRAP 1.5 – Software Tool for Rapid Annotation of Proteins

STRAP 1.5

:: DESCRIPTION

STRAP, the Software Tool for Rapid Annotation of Proteins, saves you time by automatically annotating a protein list with information that helps you meaningfully interpret your mass spectrometry data.

::DEVELOPER

Cardiovascular Proteomics Center ,BU School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 STRAP

:: MORE INFORMATION

Citation

Bhatia VN, Perlman DH, Costello CE, McComb ME.
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.
Analytical Chemistry 2009, 81 (23), 9819-23.

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

VaLiAnT – Variant Library Annotation Tool

VaLiAnT

:: DESCRIPTION

VaLiAnT is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments.

::DEVELOPER

CASM IT

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

VaLiAnT

:: MORE INFORMATION

Citation

Barbon L, Offord V, Radford EJ, Butler AP, Gerety SS, Adams DJ, Tan HK, Waters AJ.
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments.
Bioinformatics. 2021 Nov 16:btab776. doi: 10.1093/bioinformatics/btab776. Epub ahead of print. PMID: 34791067.

MAKER v3.01.03 – Genome Annotation pipeline

MAKER v3.01.03

:: DESCRIPTION

MAKER is a portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER’s inputs are minimal and its ouputs can be directly loaded into a GMOD database.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAKER

:: MORE INFORMATION

Citation:

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19.
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M.

fLPS 2.0 – rapid Annotation of Compositional Biases in Biological Sequences

fLPS 2.0

:: DESCRIPTION

fLPS is a package for the annotation of Compositional Biases (CB) regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA.

::DEVELOPER

Paul Martin Harrison

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

fLPS

:: MORE INFORMATION

Citation

Harrison PM.
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences.
PeerJ. 2021 Oct 28;9:e12363. doi: 10.7717/peerj.12363. PMID: 34760378; PMCID: PMC8557692.

MINTIA v1.0 – Metagenomic INsertT BIoinformatic Annotation

MINTIA v1.0

:: DESCRIPTION

MINTIA is a software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories.

::DEVELOPER

MINTIA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Perl

:: DOWNLOAD

MINTIA

:: MORE INFORMATION

Citation

Bardou P, Laguerre S, Maman Haddad S, Legoueix Rodriguez S, Laville E, Dumon C, Potocki-Veronese G, Klopp C.
MINTIA: a metagenomic INserT integrated assembly and annotation tool.
PeerJ. 2021 Sep 27;9:e11885. doi: 10.7717/peerj.11885. PMID: 34692239; PMCID: PMC8483015.