Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

CATCHprofiles | Clustering and alignment tool for ChIP profiles

Troubles

A standalone for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns ‘‘ab initio’’, and enables the detection of new patterns from ChIP data at a high resolution, exemplified by the detection of asymmetric histone and histone modification patterns around H2A.Z-enriched sites. CATCHprofiles’ capability for exhaustive analysis combined with its ease-of-use makes it an invaluable tool for explorative research based on ChIP profiling data.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

CATCHprofiles forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

CATCHprofiles classification

CATCHprofiles specifications

Unique identifier:
OMICS_02171
Software type:
Application/Script
Restrictions to use:
None
Input format:
WIG, BED
Output format:
CATCH, CSV, BED, NEWICK
Programming languages:
C, Java
Version:
3.0
Maintained:
Yes
Name:
Clustering and AlignmenT of ChIp profiles
Interface:
Graphical user interface
Input data:
Selected areas from the ChIP profiling data, e.g. areas obtained from peak calling, or areas selected from annotation, such as promoter regions
Output data:
Profile patterns, positions, cluster tree
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Medium
Stability:
Stable

CATCHprofiles distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

CATCHprofiles support

Documentation

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands; Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark; Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, Netherlands; eScience Centre, University of Copenhagen, Copenhagen, Denmark

Funding source(s)

This work was funded in part by the European HEROIC project for epigenetic research (EU FP6 Integrated Project), by the Stichting Nationale Computerfaciliteiten (National Computing Facilities Foundation, NCF), by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organization for Scientific Research, NOW).

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.