Tag: Genomic Region

MotifScan 1.3.0 – Scan input Genomic Regions with known DNA motifs

MotifScan 1.3.0

:: DESCRIPTION

Given a set of input genomic regions, MotifScan scans the sequences to detect the occurrences of known motifs. It can also applies a statistical test on each motif to check whether the motif is significantly over- or under-represented (enriched or depleted) in the input genomic regions compared to another set of control regions.

::DEVELOPER

ShaoLab at CAS-MPG Partner Institute for Computational Biology, SIBS, CAS.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MotifScan

:: MORE INFORMATION

Citation

Sun, H., Wang, J., Gong, Z. et al.
Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters.
Cell Discov 4, 38 (2018).

CREAM 1.1.1 – Clustering of Genomic Regions Analysis Method

CREAM 1.1.1

:: DESCRIPTION

CREAM (Clustering of Genomic Regions Analysis Method) provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). ‘CREAM’ uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. ‘CREAM’ considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 CREAM

:: MORE INFORMATION

 

ADMIRE v1.1.0 – Analysis of DNA Methylation in Genomic Regions

ADMIRE v1.1.0

:: DESCRIPTION

ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K and Infinium MethylationEpic assays.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ADMIRE

:: MORE INFORMATION

Citation:

Preussner J, Bayer J, Kuenne C and Looso M.
ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay.
Epigenetics Chromatin, 8, 51(2015), doi:10.1186/s13072-015-0045-1

BLAST2GENE – Gene Analysis in Genomic Regions

BLAST2GENE

:: DESCRIPTION

BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 BLAST2GENE

:: MORE INFORMATION

Citation

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama M, Torrents D, Bork P
Bioinformatics. 2004 Aug 12; 20(12): 1968-70. Epub 2004 Mar 22; PubMed: 15037510.

ADHoRe – Detect Genomic Regions

ADHoRe

:: DESCRIPTION

ADHoRe (Automatic Detection of Homologous Regions) is a software tool that automatically detects genomic regions with statistically significant conserved gene content and order.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Perl

:: DOWNLOAD

 ADHoRe

:: MORE INFORMATION

Citation

Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002)
The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice.
Genome Res. 12, 1792-801.