Tag: Coordinate

COCOA 2.8.0 – Coordinate Covariation Analysis

COCOA 2.8.0

:: DESCRIPTION

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

COCOA

:: MORE INFORMATION

Citation

Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC.
COCOA: coordinate covariation analysis of epigenetic heterogeneity.
Genome Biol. 2020 Sep 7;21(1):240. doi: 10.1186/s13059-020-02139-4. PMID: 32894181; PMCID: PMC7487606.

Kraken 1.0 – Genomic Coordinate Translator for Comparative Genomics

Kraken 1.0

:: DESCRIPTION

Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.
A universal genomic coordinate translator for comparative genomics.
Zamani N1, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

MEDELLER – Homology-Based Coordinate Generation for Membrane Proteins

MEDELLER

:: DESCRIPTION

MEDELLER, a MP(Membrane proteins)-specific homology-based coordinate generation method,  which is optimized to build highly reliable core models.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2833-40. doi: 10.1093/bioinformatics/btq554. Epub 2010 Oct 5.
MEDELLER: homology-based coordinate generation for membrane proteins.
Kelm S, Shi J, Deane CM.

Hybsweeper 02 – Detect High-density Plate Gridding Coordinates

Hybsweeper 02

:: DESCRIPTION

 Hybsweeper was developed to handle images of high-density gridding patterns which were matched to clones housed in microtiter dishes. As high-throughput methodologies contribute to large archives of stored clone resources, methods need to be available for convenient processing of hybridization information for the retrieval of the clones needed for research endeavors. A Java software package, Hybsweeper, was developed to select clone identities from autoradiographs which were generated through simple probing methods, overgo probe hybridizations, and isolation of unique clones from saturation hybridization.

::DEVELOPER

Gerard R. Lazo

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  Hybsweeper

:: MORE INFORMATION

Citation

Gerard R. Lazo, Nancy Lui, Yong Q. Gu, Xiuying Kong, Devin Coleman-Derr, and Olin D. Anderson.
Hybsweeper: a resource for detecting high-density plate gridding coordinates
BioTechniques (2005) 39:320-324.

UnGraph 5 – Digitizer Program Which Gives X,Y Coordinates of Lines or Points on Scanned Images

UnGraph 5

:: DESCRIPTION

UnGraph is TWAIN compliant, giving the option to scan images directly from within the software. UnGraph can also directly import images in many formats including TIF, PCX, JPG, BMP and TGA. Images can be panned and zoomed to view and vectorize selected portions. Paint, replace and erase tools allow you to modify images at any time.

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

UnGraph

:: MORE INFORMATION

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