Description
Name Description
Program MoRAine is a tool for the reannotation of transcription factor binding motifs and the creation of sequence logos.

It reasseses the given binding sequences, by switching the strand annotations, and by shifting the motifs in order to maximize the information content of the corresponding position specific scoring matrix.
Release 2.0
Developers MoRAine 2.0: Tobias Wittkop (CeBiTec, Bielefeld University), Jan Baumbach (ICSI, UC Berkely)
MoRAine 1.0: TW, JB, Jochen Weile (Newcastle University), Sven Rahmann (TU Dortmund)
Clustering The recent release 2.0 utilizes Transitivity Clustering internally to improve running time and accuracy compared to MoRAine 1.0.
Sequence logos For painting sequence logos, MoRAine utilizes the Berkeley WebLogo library by Crooks et al.
Download MoRAine is open source and can be downloaded here as java JAR file.
Publication/citation MoRAine 2.0: not published yet
MoRAine 1.0: Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. Journal of Integrative Bioinformatics, 5(2):91, 2008. (download).

Input
Option Value
Transcription factor binding sites (in FASTA format)
Allowed shifts to the left
Allowed shifts to the right


Sequence logo with (cm)
Sequence logo height (cm)
Sequence logo title





Examples:

Description Sequences
Transcription factor binding sites of NarL (E.coli) (in FASTA format). Using standard options and left/right = 0 for motif reannotation.

Description Sequences
Transcription factor binding sites of NarL (E.coli) (in FASTA format). Using standard options and left/right = 1 for motif reannotation.

Description Sequences
Transcription factor binding sites of MalT (E.coli) (in FASTA format). Using standard options and left/right = 0 for motif reannotation.