Tag: Orientation

ScaffoldScaffolder 0.1 – Solving Contig Orientation via Bidirected to Directed Graph Reduction

ScaffoldScaffolder 0.1

:: DESCRIPTION

ScaffoldScaffolder is a stand-alone scaffolding algorithm which was designed specifically for scaffolding diploid genomes.

::DEVELOPER

Computational Science Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA

:: DOWNLOAD

 ScaffoldScaffolder

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 7:S5. doi: 10.1186/1471-2105-16-S7-S5. Epub 2015 Apr 23.
Heterozygous genome assembly via binary classification of homologous sequence.
Bodily PM, Fujimoto M, Ortega C, Okuda N, Price JC, Clement MJ, Snell Q.

ScaffoldScaffolder: Solving Contig Orientation via Bidirected to Directed Graph Reduction.
Bodily PM, Fujimoto MS, Snell Q, Ventura D, Clement MJ.
Bioinformatics. 2015 Sep 17. pii: btv548.

ProtPOS 1.1 – Fast Prediction of Protein Preferred Orientation on a Surface

ProtPOS 1.1

:: DESCRIPTION

ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption.

::DEVELOPER

Computational Biology and Bioinformatics Lab (CBBio)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • Python

:: DOWNLOAD

ProtPOS

:: MORE INFORMATION

Citation

Ngai JC, Mak PI, Siu SW.
ProtPOS: a python package for the prediction of protein preferred orientation on a surface.
Bioinformatics. 2016 Aug 15;32(16):2537-8. doi: 10.1093/bioinformatics/btw182. Epub 2016 Apr 10. PMID: 27153619; PMCID: PMC4978930.

memembed 1.15 – Membrane Protein Orientation Predictor

memembed 1.15

:: DESCRIPTION

memembed is a software of membrane protein orientation and refinement using a knowledge-based statistical potential

::DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 memembed

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013 Sep 18;14:276. doi: 10.1186/1471-2105-14-276.
Membrane protein orientation and refinement using a knowledge-based statistical potential.
Nugent T1, Jones DT.

TMpred 1.0 – Prediction of Transmembrane Regions and Orientation

TMpred 1.0

:: DESCRIPTION

The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins

::DEVELOPER

EMBnet

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TMpred

:: MORE INFORMATION

Citation:

K. Hofmann & W. Stoffel (1993)
TMbase – A database of membrane spanning proteins segments
Biol. Chem. Hoppe-Seyler 374,166