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DNA SCANNER is a tool which scans DNA for
number of different properties such as biophysical, energy, potential for
protein interactions and sequence based features such as T density, AT
density etc. It scans the DNA through sliding window mechanism. The
tool gives user a number of properties to scan and therefore analysis of
DNA sequence is not limited to homology searches such as blast, finding
sequence based patterns, GC % etc. Its a easy to use yet very useful
tool for researchers wishing to understand more about their DNA sequence.
DNA SCANNER has wide applicability in analysis of DNA sequences. One
may like to analyse promoter, repeats, retroviral , insertion sites of
retrotransposons, genic, intergenic, intron exon boundaries
sequences to name a few. (Click here
to read more)
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Please make sure sequences are in fasta
format.
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The sequences should be of same
length.
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Sequences should not have non DNA
characters.
Please Paste your sequence(s) in fasta format (Help).
Sample
Data of Alu preinsertion sites in Human Genome
Please enter window size for searching: (Default:5 bp )
(Help in
deciding window size ?)
Please enter start position for plotting (Default:
-40 ) (Help
?)
What are the parameters you would search for?
Sequence
Based Parameters
Trule
Arule
Grule Crule ATrule
Physicochemical
Properties
Bendability
Nucleosomal Positioning
B
form to A form transition
Propeller Twist
Bending Stiffness
Protein Induced Deformability
Energy
Parameters
DNA Denaturation Duplex
Stability Stabilizing Energy
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