Tag: Genome

MOSGA 2 – Modular Open-Source Genome Annotator

MOSGA 2

:: DESCRIPTION

The MOSGA is a pipeline that easily creates draft genome annotation by a graphical user interface. It combines several specific prediction tools and generates a submission-ready annotation file.

::DEVELOPER

MOSGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MOSGA

:: MORE INFORMATION

Citation

Martin R, Hackl T, Hattab G, Fischer MG, Heider D.
MOSGA: Modular Open-Source Genome Annotator.
Bioinformatics. 2021 Apr 1;36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003. PMID: 33258916.

Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D.
MOSGA 2: Comparative genomics and validation tools.
Comput Struct Biotechnol J. 2021 Sep 28;19:5504-5509. doi: 10.1016/j.csbj.2021.09.024. PMID: 34712396; PMCID: PMC8517542.

 

SatFind – C-program for Finding Satellites in Genomes

SatFind

:: DESCRIPTION

SatFind – C-program for Finding Satellites in Genomes

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C compiler

:: DOWNLOAD

 SatFind

:: MORE INFORMATION

Citation

PLoS One. 2013 Apr 24;8(4):e62221. doi: 10.1371/journal.pone.0062221.
A satellite explosion in the genome of holocentric nematodes.
Subirana JA, Messeguer X.

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.

Gclust 3.5.5z3 – Genome-wide Clustering

Gclust 3.5.5z3

:: DESCRIPTION

Gclust software was developed to make clusters of protein sequences from all predicted protein sequences in a selected set of genomes.

::DEVELOPER

Sato Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C++ Compiler

:: DOWNLOAD

  Gclust

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):599-605. doi: 10.1093/bioinformatics/btp047.
Gclust: trans-kingdom classification of proteins using automatic individual threshold setting.
Sato N.

CTRD – Computing Translocation Distance between Genomes

CTRD

:: DESCRIPTION

CTRD (Computing Translocation Distance between Genomes) computes the translocation distance between two signed genomes. It takes two genomes as its input and tests whether one genome can be transformed into the other. If possible, it computes the translocation distance between two genomes, and gives the translocation operation serial.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /Linux/MacOsX
  • Java

:: DOWNLOAD

 CTRD

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Nov 22;20(17):3256-7. Epub 2004 Jun 16.
CTRD: a fast applet for computing signed translocation distance between genomes.
Feng W, Wang L, Zhu D.

miRe2e – Finding pre-miRNA sequences in raw Genome-wide data

miRe2e

:: DESCRIPTION

miRe2e is a novel deep learning model based on Transformers that allows finding pre-miRNA sequences in raw genome-wide data.

::DEVELOPER

Research institute for signals, systems and computational intelligence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

miRe2e

:: MORE INFORMATION

Citation:

Raad J, Bugnon LA, Milone DH, Stegmayer G.
miRe2e: a full end-to-end deep model based on Transformers for prediction of pre-miRNAs.
Bioinformatics. 2021 Dec 7:btab823. doi: 10.1093/bioinformatics/btab823. Epub ahead of print. PMID: 34875006.

Refgenie v0.12.1 / refgenieserver v0.7.0 – Reference Genome Resource Manager

Refgenie v0.12.1 / refgenieserver v0.7.0

:: DESCRIPTION

Refgenie manages storage, access, and transfer of reference genome resources.

Refgenieserver is containerized code that hosts genome assets that can be automatically downloaded by the refgenie command-line interface.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Refgenie / Refgenieserver

:: MORE INFORMATION

Citation

Stolarczyk M, Reuter VP, Smith JP, Magee NE, Sheffield NC.
Refgenie: a reference genome resource manager.
Gigascience. 2020 Feb 1;9(2):giz149. doi: 10.1093/gigascience/giz149. PMID: 31995185; PMCID: PMC6988606.

PaKman – Parallel Genome Assembler for Scalable Generation of Genomic Contigs

PaKman

:: DESCRIPTION

PaKman is a scalable algorithm for generating genomic contigs on distributed memory machines.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

PaKman

:: MORE INFORMATION

Citation

Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.

Varclus – Detection of Positive Selection in Genes and Genomes through Variation Clusters

Varclus

:: DESCRIPTION

Varclus is a perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 Varclus

:: MORE INFORMATION

Citation:

Wagner, A. (2007)
Rapid detection of positive selection in genes and genomes through variation clusters.
Genetics 176: 2451–2463

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.

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