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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Create Alignment Seeds

FLAK allows any seed to be defined with a seed weight ≥8 and a length ≤32. To create a new seed or edit an existing seed, select the Fuzzy Seeds button (Fuzzy Seeds) on the toolbar of the main window. This will open the following dialogue box that displays a list of the existing fuzzy seeds (seed pattern and seed name). The buttons at the bottom of the dialogue can be used to create, edit or delete a fuzzy seed.

Fuzzy Seed Manager

 

If a new or edit option is chosen, a seed can be created using in the following dialogue that will be displayed:

Fuzzy Seed Dialogue

 

FLAK requires that the "must-match" positions in a seed are denoted with a hash symbol (#) and "don't care" positions by a hyphen (-). By combining these symbols FLAK can be configured with any consecutive or spaced-seed pattern with a seed weight ≥8 and a length ≤32. For example, the pattern ######## defines a BLAST-like consecutive seed of weight 10 and the pattern ###-#--#-#--##-### defines the 18 weight spaced-seed used by the original version of PatternHunter. If the length of the seed is <32, FLAK will add the required amount of don't-care positions as a prefix to the seed pattern. For convenience, it is good practice to include the seed weight and length in the seed name.

The set of seeds used by FLAK are stored in the file conf/seeds.xml in the FLAK home directory. Changes to the set of seeds used by FLAK can also be made by editing this file directly.

<?xml version="1.0" encoding="UTF-8"?>
<flak-config>
  <fuzzy-seeds>
    <seed>
      <seed-name>9/15 Choi et al. (2004)</seed-name>
      <pattern>##-##-#-#---###</pattern>
    </seed>
    <seed>
      <seed-name>10/16 Choi et al. (2004)</seed-name>
      <pattern>##-##---##-#-###</pattern>
    </seed>
    <seed>
      <seed-name>11/18 PatternHunter. Ma et al. (2002)</seed-name>
      <pattern>###-#--#-#--##-###</pattern>
    </seed>
    <seed>
      <seed-name>12/19 Mak and Benson</seed-name>
      <pattern>####-#-#--##--#-###</pattern>
    </seed>
    <seed>
      <seed-name>13/20 Mak and Benson</seed-name>
      <pattern>####-#--##--##-#-###</pattern>
    </seed>
  </fuzzy-seeds>
</flak-config>

The normal rules for a well-formed XML document apply to this file. If you are unsure of these rules, you should use the FLAK GUI to created and edit seeds.

 

 

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