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.

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0 – PCR Primer Design Tool

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0

:: DESCRIPTION

Primer3 is a widely used program for designing PCR primers (PCR = “Polymerase Chain Reaction”). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

Primer3-web is the original web-interface to Primer3.

Primer3Plus is an updated, task-oriented web-interface to Primer3.

::DEVELOPER

developed at Whitehead_Institute and Howard Hughes Medical Institute by Steve Rozen and Helen Skaletsky.

:: SCREENSHOTS

:: REQUIREMENTS

    • Linux / Windows / Mac OsX

:: DOWNLOAD

Primer3

:: MORE INFORMATION

Citation

Steve Rozen and Helen J. Skaletsky (2000)
Primer3 on the WWW for general users and for biologist programmers.
In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386

mfinder 1.21 – Network Motifs Detection tool

mfinder 1.21

:: DESCRIPTION

mfinder is a software tool for network motifs detection.

::DEVELOPER

Uri Alon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 mfinder

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jul 22;20(11):1746-58. Epub 2004 Mar 4.
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
Kashtan N, Itzkovitz S, Milo R, Alon U.

SBRT 2.0.0 – The Systems Biology Research Tool

SBRT 2.0.0

:: DESCRIPTION

SBRT (Systems Biology Research Tool) is a software to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBRT

:: MORE INFORMATION

Citation

The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright and Andreas Wagner
BMC Systems Biology 2008, 2:55

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.

DISSECT 1.0.2 – Transcriptome-to-Genome Alignment Tool

DISSECT 1.0.2

:: DESCRIPTION

Dissect (DIScovery of Structural Alteration Event Containing Transcripts) is a transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  DISSECT

:: MORE INFORMATION

Citation

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics. 2012 Jun 15;28(12):i179-87

Sibelia 3.0.7 – Synteny Block ExpLoration tool

Sibelia 3.0.7

:: DESCRIPTION

Sibelia is a comparative genomic tool。 It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments.

::DEVELOPER

Algorithmic Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows

:: DOWNLOAD

 Sibelia

:: MORE INFORMATION

Citation

F1000Res. 2013 Nov 25;2:258. doi: 10.12688/f1000research.2-258.v1. eCollection 2013.
C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.
Minkin I, Pham H, Starostina E, Vyahhi N, Pham S

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham.
Sibelia: A fast synteny blocks generation tool for many closely related microbial genomes
(submitted)

OptiMAS 1.5 – Decision Support tool to conduct Marker-Assisted Selection programs

OptiMAS 1.5

:: DESCRIPTION

OptiMAS has been developed with the possibility to consider a multi-allelic context,which opens new prospects to further accelerate genetic gain by assembling favorable alleles issued from diverse parents.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

OptiMAS

:: REQUIREMENTS

  •  Windows / Linux / MacOsX

:: DOWNLOAD

 OptiMAS

:: MORE INFORMATION

Citation:

Valente, F., Gauthier, F., Bardol, N., Blanc, G., Joets, J., Charcosset, A. & Moreau, L. (in prep)
OptiMAS: decision support for marker-assisted selection.

PGDSpider 2.1.1.5 – Data conversion tool for Population Genetic and Genomics Programs

PGDSpider 2.1.1.5

:: DESCRIPTION

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • java

:: DOWNLOAD

 PGDSpider

:: MORE INFORMATION

Citation

Lischer HEL and Excoffier L (2012)
PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs.
Bioinformatics 28: 298-299.

cERMIT v1.2 – the Evidence Ranked Motif Identification Tool

cERMIT v1.2

:: DESCRIPTION

cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  cERMIT

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(2):R19. doi: 10.1186/gb-2010-11-2-r19. Epub 2010 Feb 15.
Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U.