Tag: Precise

preciseTAD 1.4.0 – Machine Learning framework for precise TAD Boundary Prediction

preciseTAD 1.4.0

:: DESCRIPTION

preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution.

::DEVELOPER

Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R
  • BioConductor

:: DOWNLOAD

preciseTAD

:: MORE INFORMATION

Citation:

Stilianoudakis SC, Marshall MA, Dozmorov MG.
preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution.
Bioinformatics. 2021 Nov 6:btab743. doi: 10.1093/bioinformatics/btab743. Epub ahead of print. PMID: 34741515.

Precise – Predict Regulatory Cis-acting Elements

Precise

:: DESCRIPTION

PRECISE can predict regulatory cis-acting elements through DNA sequences. It aimed at advanced mining of specific biological data: sequence data of DNA sequences that lie upstream of regions with known coding function.

PRECISE performs an extensive (and computation time intensive) search and comparison through these DNA sequences to look for common fragments (motifs, boxes).

PRECISE highlights common fragments and can yield a complete presence/absence table for all found boxes and sequences which an be used for further statistical analysis.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Precise

:: MORE INFORMATION

Citation

PRECISE: software for prediction of cis-acting regulatory elements.
Trindade LM, van Berloo R, Fiers M, Visser RG.
J Hered. 2005 Sep-Oct;96(5):618-22. Epub 2005 Aug 31.