BaMMmotif

August 9th 2018: We updated the server to version 1.4.0. (Changelog)

Results for example run

Refined Motifs

#	IUPAC	PWM	reverse Comp.	motif AvRec	frac. occurrence	Download
1	AGGRTGASTCA			0.839	0.978
2	GGRTGACT			0.442	0.956
3	SSYGGGCG			0.733	0.035

Motif # 1

Motif Performance and Motif Distribution on Sequences

Best matches with our motif database

name	e-value	query motif	database PWM	reverse Comp.	DB Entry
Fra-2	1.8E-03
JunD	1.9E-03
Fra-1	1.9E-03
JunB	2.8E-03
SMARCC1	2.9E-03

Motif # 2

Motif Performance and Motif Distribution on Sequences

Best matches with our motif database

name	e-value	query motif	database PWM	reverse Comp.	DB Entry
JunD	1.6E-02
SMARCC1	1.7E-02
c-Jun	2.1E-02
Fra-1	2.2E-02
c-Fos	3.1E-02

Motif # 3

Motif Performance and Motif Distribution on Sequences

Best matches with our motif database

name	e-value	query motif	database PWM	reverse Comp.	DB Entry
KLF7	4.3E-01
DbpA	4.8E-01

Tool settings

General settings

Job id:	00000000-0000-0000-0000-000000000004
Input sequences:	ExampleData.fasta
Search on both strands:	True
Background Sequences:	not set
Background Model Order:	2

Seeding stage

Pattern Length:	8
Z-Score Threshold:	10.0
Count Threshold:	5
IUPAC Optimization Score:	MUTUAL_INFO
Skip EM:	False

Refinement stage

Model Order:	2
Flank extension:	0

Additional settings

Run motif scanning:	True
Motif scanning p-value cutoff:	0.0001
Run motif evaluation:	True
Run motif-motif compare:	True
MMcompare database:	GTRD_v1804_HUMAN
MMcompare e-value cutoff:	0.50