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Virtual Footprint logo Version 3.0 Virtual Footprint logo

Step 1: Input DNA Sequence...

Sequence
  Select PRODORIC Genome/Replicon:
 Genome/Replicon
  Upload FASTA Sequence
 FASTA File
  Paste Raw Sequence
 Paste Sequence [Clear]

Step 2: Input Pattern...

Pattern Definition
 Single Pattern  Bipartite Pattern
 Name/Orientation:  Ignore Subpattern Orientation    Ignore Subpattern Orientation  
 Subpattern Type:   Position Weight Matrix   Position Weight Matrix
 Library:
 Position Weight Matrix:
 Custom PWM:
(Paste FASTA sequences)
[Clear] [Clear]
 PWM Options  Non-Occurance Penalty   Non-Occurrence Penalty 
 Sensitivity/Threshold:  0.7-1.0    (optionally)  0.7-1.0    (optionally)    (cumulative threshold)
 Core Sensitivity/Size:  0.6-1.0    1-6  0.6-1.0    1-6
 Weight Matrix Information:
 Subpattern Type:   IUPAC Code   IUPAC Code
 Sequence:  (IUPAC Code)  (IUPAC Code)
 Mismatches:
 Subpattern Type:   Regular Expression   Regular Expression
 Regular Expression
Subpattern distance
 Spacer: Minimal Space:   (0-50 bp) Maximal Space:   (0-50 bp)

Step 3: Enter Search Options and Start Searching...

Start Searching
 Promoter Length Maximum Distance to Gene:   bp 
 Match Properties  Restrict to Noncoding (Intergenic) Regions    Ignore Match Orientation (Strand)    Remove Redundant (Palindromic) Matches  
 Result Sorting  Order By Genomic Position  Order By Score

© 2003-2008 by Richard Münch •  Institute of Microbiology • Technical University of Braunschweig •  r.muench(at)tu-bs.de