iORI-PseKNC 2.0 – Identify ORIs in the Saccharomyces cerevisiae Genome

iORI-PseKNC 2.0

:: DESCRIPTION

iORI-PseKNC is a server for the prediction of the initiated site of DNA replication based on machine learning method. The initiation of replication origin is an extremely important process of DNA replication. The distribution of replication origin regions (ORIs) is the major determinant of the timing of genome replication. Thus, correctly identifying ORIs is crucial to understand DNA replication mechanism.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique.
Dao FY, Lv H, Wang F, Feng CQ, Ding H, Chen W, Lin H.
Bioinformatics. 2019 Jun 1;35(12):2075-2083. doi: 10.1093/bioinformatics/bty943.

iRSpot-Pse6NC 2.0 – Identifying Recombination Hotspots in Saccharomyces Cerevisiae

iRSpot-Pse6NC 2.0

:: DESCRIPTION

Based on dataset containing both ORF and non-ORF recombination sites, iRSpot-Pse6NC is a predictor which using SVM classifier by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution feature selection approach.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae.
Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H.
Brief Bioinform. 2019 Oct 21. pii: bbz123. doi: 10.1093/bib/bbz123

iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC.
Int J Biol Sci. 2018 May 22;14(8):883-891. doi: 10.7150/ijbs.24616. eCollection 2018.
Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H.

m6Apred – Identification and Analysis of the N6-methyladenosine in Saccharomyces Cerevisiae Transcriptome

m6Apred

:: DESCRIPTION

The web-server m6Apred was developed to identify the N6-methyladenosine (m6A).

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome.
Chen W, Tran H, Liang Z, Lin H, Zhang L.
Sci Rep. 2015 Sep 7;5:13859. doi: 10.1038/srep13859.

YPA 1.6 – Repository of Promoter features in Saccharomyces cerevisiae

YPA 1.6

:: DESCRIPTION

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene expression data) and provides a comprehensive view of the promoter regions.

::DEVELOPER

Molecular Biomedical Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borowser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Darby Tien-Hao Chang, Cheng-Yi Huang, Chi-Yeh Wu, and Wei-Sheng Wu,
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae“,
Nucleic Acids Res. 2011 39: D647-D652.