IPPI – Inferring Protein-Protein Interactions for YEAST

IPPI

:: DESCRIPTION

IPPI is a web server of inferring protein-protein interactions

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Oct;19 Suppl 2:ii58-65.
Inferring strengths of protein-protein interactions from experimental data using linear programming.
Hayashida M, Ueda N, Akutsu T.

LRSDAY v1.6.0 – Long-read Sequencing Data Analysis for Yeasts

LRSDAY v1.6.0

:: DESCRIPTION

LRSDAY is a highly transparent, automated and powerful computational framework for high-quality genome assembly and annotation.

::DEVELOPER

Jia-Xing Yue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LRSDAY

:: MORE INFORMATION

Citation

Yue JX, Liti G.
Long-read sequencing data analysis for yeasts.
Nat Protoc. 2018 Jun;13(6):1213-1231. doi: 10.1038/nprot.2018.025. Epub 2018 May 3. PMID: 29725120.

YGOB v7 – Yeast Gene Order Browser

YGOB v7

:: DESCRIPTION

YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Res. 2005 Oct;15(10):1456-61. Epub 2005 Sep 16.
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.
Byrne KP1, Wolfe KH.

YGAP – Yeast Genome Annotation Pipeline

YGAP

:: DESCRIPTION

YGAP is an online tool to annotate yeast species based on sequence and synteny conservation.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.
Proux-Wéra E1, Armisén D, Byrne KP, Wolfe KH.

Bagheera – Predicting Fungal CUG Codon Translation in Yeast

Bagheera

:: DESCRIPTION

Bagheera is a web server of prediction of genes in yeast species by providing the correct CUG decoding scheme , that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data.

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 May 29;15:411. doi: 10.1186/1471-2164-15-411.
Predicting the fungal CUG codon translation with Bagheera.
Mühlhausen S, Kollmar M

YEASTRACT / YEASTRACT-DISCOVERER – Yeast Search for Transcriptional Regulators And Consensus Tracking

YEASTRACT / YEASTRACT-DISCOVERER

:: DESCRIPTION

YEASTRACT is a curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references.

YEASTRACT-DISCOVERER is a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes.

::DEVELOPER

YEASTRACT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.
Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, Dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT, Sá-Correia I.
Nucl. Acids Res. (2013)doi: 10.1093/nar/gkt1015

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.
Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenço AB, dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, Sá-Correia I, Freitas AT.
Nucleic Acids Res. 2011 Jan;39(Database issue):D136-40. doi: 10.1093/nar/gkq964.

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.
Monteiro PT, Mendes ND, Teixeira MC, d’Orey S, Tenreiro S, Mira NP, Pais H, Francisco AP, Carvalho AM, Louren?o AB, Sá-Correia I, Oliveira AL, Freitas AT.
Nucleic Acids Res. 2008 Jan;36(Database issue):D132-6.

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.
Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D446-51.

Chromatin Cutter 1.00 – Simulates the distribution of DNA in a Gel Electrophoresis Study of Yeast Chromatin cut by Enzymes

Chromatin Cutter 1.00

:: DESCRIPTION

Chromatin Cutter simulates the distribution of DNA in a gel electrophoresis study of Yeast chromatin cut by enzymes. It lets you specify the fraction of nucleosomes that are unwrapped (wrapped ones have inaccessible DNA). It lets you specify the variance in the distribution of nucleosomes around their mean distance. It lets you specify the number of cuts per unit length (enzyme concentration). It plots the effects of these on the log number of base pairs, which matches the gel electrophoresis mass distribution.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

ChromatinCutter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Chromatin Cutter

:: MORE INFORMATION

YeastSpotter 2.1 – Yeast Segmentation Web Tool

YeastSpotter 2.1

:: DESCRIPTION

YeastSpotter is a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.

::DEVELOPER

Alan Moses’ Computational Biology Lab,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

YeastSpotter

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 1;35(21):4525-4527. doi: 10.1093/bioinformatics/btz402.
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.
Lu AX, Zarin T, Hsu IS, Moses AM

nucloc 1.06 – Analyzing Gene Positions in the Yeast Nucleus

nucloc 1.06

:: DESCRIPTION

nucloc is a set of computational tools designed to analyze gene positioning in yeast nuclei by automated processing of fluorescence microscopy images.

::DEVELOPER

Computational Imaging & Modeling Group,  Institut Pasteur

:: SCREENSHOTS

nucloc

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Matlab

:: DOWNLOAD

 nucloc

:: MORE INFORMATION

Citation:

Nat Methods. 2008 Dec;5(12):1031-7. doi: 10.1038/nmeth.1266. Epub 2008 Nov 2.
High-resolution statistical mapping reveals gene territories in live yeast.
Berger AB, Cabal GG, Fabre E, Duong T, Buc H, Nehrbass U, Olivo-Marin JC, Gadal O, Zimmer C.