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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Protein location
RNA structure
Protein structure
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs



Comparison of nucleotide sequences

SCAN2 - program for aligning two multimegabyte-size genome sequences (with Java viewer [Help]).

To view human genome in our Genome Explorer, click here - you can also map your sequence by FMAP in that graphical interface. To view mouse genome, click here.

Paste first sequence in here:

or select local file:

Paste second sequence in here:

or select local file:

Choose method:

Normal similarity (fast)
Weak similarity (for promoter seq comparison, up to 10000 bp recommended for WEB)

No dynamic programming
Global alignment with tail gaps by dynamic programming
Global alignment without tail gaps by dynamic programming
Local alignment by dynamic programming

Block info only
Fine alignment
Alignment bounds, Block info and fine alignment

In direct chain only
In reverse chain only
In both chains

Use Java viewer

Note. To run applet viewer you need to include linux1.softberry.com in the list of your browser (see instruction).

Please note that using option based on dynamic programming with big sequences is very slow.

[Help] [Show advanced options
[Example w/o visualization]

Return to page with other programs of group: Alignment / Sequences & genomes

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Last modification date: 19 Mar 2015

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