Sequences

Input to this visualization program can be given either as fasta formatted DNA sequence (s) or as a file that contains fasta formated DNA sequence(s). Fasta format contains a definition line and a sequence. The definition line starts with a right angle bracket (>). See the example below.

>sequence 1
actgtgtgtgtgtgactcgtgccctggctgcgtcgtcgtcgtcgctgct.....


Patterns to search for

Search patterns are inserted into the box provided. The search patterns contain usually letters coding for nucleotides (a, c, t, g) but can also contain letters defined in the IUPAC code.

codedescriptioncodedescription
AAdenine KT, U, or G
CCytosine WT, U, or A
GGuanineSC or G
TThymineBC, T, U, or G (not A)
UUracilDA, T, U, or G (not C)
RPurine (A or G) HA, T, U, or C (not G)
YPyrimidine (C, T, or U) VA, C, or G (not T, not U)
MC or ANAny base (A, C, G, T, or U)

Sequence length

The sequence length given defines the length of the sequence visualized. The maximum sequence length recommended is 3000 bp, although you can visualize sequences longer than this. The sequences are thought to be given in 5' -> 3' direction. If sequence is longer than the sequence length given, the additional sequence part is cut away from the 5' point end of the sequence.


Ignore overlapping patterns
Are overlapping patterns reported or not.



This tool was developed by Matti Kankainen, University of Helsinki
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© 2006 University of Helsinki