Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment
Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment   Download FLAK 1.0

 

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Alignment Filtering

Unlike other genome alignment systems, FLAK allows users to filter alignment data. This can be useful if the values specified for the seed weight and minimum match length were found to be too small. The resultant visualisation of the alignment will be obfuscated by the presence of a large amount of data to display. While selecting the Cluster Alignments option on the Alignment Constraints section of the wizard will eliminate most, if not all, of this "noise", you can also filter a comparison by selecting the Filter Alignments (Filter Alignments) at the bottom of the plotter window.

Filter Alignments

Consider the example below which depicts the comparison of E.coli K12 v/s E.coli 536, with the seed ###-#--#-#--##-###, a β cut-off of 0.7, a minimal match length of 32 and no clustering. The initial visualisation (left) contains a significant amount of noise that obscures the main alignment along the central diagonal. The plot on the right is the result of applying a length filter of 33 to the same data.

Filter Alignments
E.coli K12 v/s E.coli 536.

In addition to modifying the alignment visualisation, applying a filter will also alter the output of the alignment, whether as an image or a text file. Applying a filter is revokable (unless the Delete Alignments option has been selected), i.e. users can always reset the filter to the original match length to undo any operation. If the current display is showing alignments that have been filtered, the filter button will be coloured in red:

Filter Alignments

If the Delete Alignments option is selected, the set of alignment data less than the specified length will be permanently discarded. In addition to providing a clearer visualisation of a comparison, applying the delete option will reduce the amount of memory consumed by FLAK.

 

 

© 2016.  FLAK (Fuzzy Logic Analysis of k-mers) Version 1.0     
Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment