FOG 1.0 – A tool to Map Genomic Features on to Genes

FOG 1.0 / webFOG

:: DESCRIPTION

FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.

::DEVELOPER

 Dr. Sonika Tyagi or Dr. Derek Nancarrow , Professor David Whiteman

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Perl

:: DOWNLOAD

 FOG

:: MORE INFORMATION

Citation

Sonika Tyagi, Mitchell S. Stark, Nicholas K. Hayward, David C. Whiteman and Derek J. Nancarrow.
webFOG: A web tool to Map Genomic Features on to Genes , Biochemical and Biophysical Research Communications,
Biochem Biophys Res Commun. 2010 Oct 22;401(3):447-50. Epub 2010 Sep 24.

BEDTools 2.30.0 – Compare Genomic Features

BEDTools 2.30.0

:: DESCRIPTION

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BEDGFF/GTFVCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by “streaming” several BEDTools together.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BEDTools

:: MORE INFORMATION

Citation:

Quinlan AR and Hall IM, 2010.
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 26, 6, pp. 841–842.

Phylo-HMGP – Infer Heterogeneous Evolutionary States of Functional Genomic Features

Phylo-HMGP

:: DESCRIPTION

Phylo-HMGP ( phylogenetic hidden Markov Gaussian processes) identifies evolutionary patterns from multi-species continuous functional genomic signals.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Phylo-HMGP

:: MORE INFORMATION

Citation

Cell Syst. 2018 Aug 22;7(2):208-218.e11. doi: 10.1016/j.cels.2018.05.022.
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.
Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O’Neill RJ, Gilbert DM, Ma J.

Suite16 2.1 – Co-localizes and Displays Genomic Features

Suite16 2.1

:: DESCRIPTION

Suite16 is a coherence viewer which co-localizes and displays genomic features.

::DEVELOPER

Krawetz Lab

:: SCREENSHOTS

Suite16

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 Suite16

:: MORE INFORMATION

Citation

Linnemann A. K., Platts A. E., Doggett N., Gluch A., Bode J., Krawetz S. A.
Genomewide identification of nuclear matrix attachment regions: an analysis of methods.
Biochem Soc Trans 2007; 35(Pt 3)612-617.

overlap – Compute Overlap between two sets of Genomic Features

overlap

:: DESCRIPTION

overlap is a program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set.

::DEVELOPER

Toni Hermoso Pulido

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 overlap

:: MORE INFORMATION