CisFinder: Identification of DNA over-represented motifs
Overview, Help
Array Analysis
Gene Index
Gene Expression Atlas

Description of CisFinder

CisFinder is a tool for finding over-representing short DNA motifs (e.g., transcription factor binding motifs) and estimates the Position Frequency Matrix (PFM) directly from word counts. It is designed for the analysis of ChIP-chip and ChIP-seq data and can process long input files (50 Mb). Identification and clustering of motifs takes 8 sec per 1 Mb. Other features: uses False discovery rate (FDR) and control sequences, finds motifs based on PFM.

NOTE: The error message "Operation failed!" means a suspicious command or data. Please send a message to administrator and explain the problem.

Do your own data analysis

User login:

Sign in to get a password (no restriction)
If you log in as "guest" you have full functionality in one session.
If you register, you can keep your profile, uploaded data, and generated results.

Sharov, A.A. and Ko, M.S.H. (2009). Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Research, doi: 10.1093/dnares/dsp014.

Please report any problems to webmaster

    Last modified: