Tag: Eukaryote

DisLocate – Find Disulfide bonds in Eukaryotes with predicted subcellular Localization

DisLocate

:: DESCRIPTION

 DisLocate is a a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2224-30. Epub 2011 Jun 29.
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Savojardo C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio R.

AUGUSTUS 3.4.0 – Gene Prediction for Eukaryotes

AUGUSTUS 3.4.0

:: DESCRIPTION

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server or be downloaded and run locally. It is open source so you can compile it for your computing platform.. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users.

AUGUSTUS Online Version

::DEVELOPER

Mario Stanke and Oliver Keller , Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AUGUSTUS

:: MORE INFORMATION

Citation

Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006)
“AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome”
BMC Genome Biology, 7(Suppl 1):S11.

EUPAN – Eukaryote Pan-genome ANalysis Toolkit

EUPAN

:: DESCRIPTION

EUPAN is a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Perl
  • Python

:: DOWNLOAD

EUPAN

:: MORE INFORMATION

Citation:

Bioinformatics. 2017 Aug 1;33(15):2408-2409. doi: 10.1093/bioinformatics/btx170.
EUPAN enables pan-genome studies of a large number of eukaryotic genomes.
Hu Z, Sun C, Lu KC, Chu X, Zhao Y, Lu J, Shi J, Wei C

BaCelLo – Predictor for the Subcellular Localization of Proteins in Eukaryotes

BaCelLo

:: DESCRIPTION

BaCelLo (Balanced Subcellular Localization Predictor) is a predictor for the subcellular localization of proteins in eukaryotes. It is based on a decision tree of several support vector machines (SVMs), it classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No, Only Web Service

:: MORE INFORMATION

Citation

BaCelLo: a Balanced subCellular Localization predictor.
Andrea Pierleoni 1, Pier Luigi Martelli1, Piero Fariselli1 and Rita Casadio1
Bioinformatics, 22, e408-e416.