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Gecko (version 1.2)
Query sequence file in fasta format
Reference sequence file in fasta format
Use 32 for larger sequences (above 5mbps) and 16 or smaller otherwise
The minimum length a fragment must achieve to be reported
Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)


A pairwise genome comparison software for the detection of High-scoring Segment Pairs.

GECKO (GEnome Comparison with K-mers Out-of-core) is a fast, modular application designed to identify collections of High-scoring Segment Pairs in a pairwise genome comparisons. By employing novel filtering and data storing strategies, it is able to compare chromosome-sized sequences in less time.

How to use

To use GECKO, upload two .fasta datasets and select these as "Query sequence" and as "Reference sequence". Once so, choose the parameters that best suite your comparison:

Input parameters

Output data sets

Two files are produced when running GECKO:

The CSV file can be interpreted as follows. Each column represents:


Note that fragments in the reverse strand (marked with the r field) have their yStart and yEnd coordinates switched, i.e. yEnd is smaller than yStart.