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 Output

The visualisation of alignments generated by FLAK can be outputted in either graphical or text formats:
  • Graphical: Selecting the Save Synteny Plot (Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment) button on the plotter window toolbar enables the alignment visualisation to be saved as a PNG file. The dimensions of the PNG image will match the zoom level in the plotter window.

  • Text Output The set of alignment positions in the query and reference genomes, along with the length of each alignment, can be outputted by selecting the Save Alignment Data (Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment) button on the plotter window toolbar. The file name and sort order can then be specified in the Save Alignments dialogue:

    Save Alignments

    Note that the alignment positions written to file will reflect the current state of the genome alignment visualised in the plotter window, i.e. fuzzy options (hedges and fuzzy logic) or filters applied to the visualisation will also be applied to the output.

 

Output Format

The header portion of the file provides a summary of the query parameters used in the comparison, including time, the length of the query and reference sequences, the seed pattern, β cut-off threshold and minimum match length. The body of the file contains the outputted alignment data in a tab-delimited format, using the field order: Query From, Query To, Reference From, ReferenceTo and Length. Reverse complement matches are highlighted by a trailing triplet of asterisks (***). As the alignment data outputted matches the visualised data in the plotter window, FLAK allows users to perform some post hoc experimentation on a genome comparison.

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FLAK 1.0

Query Parameters
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Time(s)=3, Qry Len=4600755, Ref Len=4600755, Overlap=0, Strand:F/R, Seed:####-#--##--##-#-###, Beta=0.85, Min Match=32bps, Filtered=No

Alignments
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Field Order:
QueryFrom QueryTo ReferenceFrom ReferenceTo Length
Reverse complements (***) have QueryFrom > QueryTo
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1 636576 1 636576 636576
3792 3823 3777 3808 32
11575 13270 355489 357184 1696
11576 13591 521953 523968 2016
11596 11659 1023969 1024032 64
11692 11915 1024065 1024288 224
11936 11745 3417409 3417600 192***
11816 15175 565057 568416 3360
17164 11821 4241409 4246752 5344***
11948 13579 1024321 1025952 1632

 

 

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