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dentearl / mafTools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
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Details on `mafStats` report #36

Open ohdongha opened 11 months ago

ohdongha commented 11 months ago

Hello, I guess the mafStats bundled in the Cactus installation (2.3.0) is from mafTools. :) If so, I have a few questions on how to read the results:

  1. Is "block area" the sum of nucleotides included in the alignments (for any species)
  2. Is "block degree" the same as "seq count in block" in the example?
  3. Is "seq field length" the number of aligned nucleotides in each row (each species), excluding gaps? Or does it include gaps and represent more of the (micro-)synteny? 
Blocks:                     107277
Ave block area:            1529.81
Max block area:              14300
Total block area:        164113820
Ave block degree:             2.05
Max block degree:               27
Ave seq field length:       737.47
Max seq field length:         1692

Thanks! Dong-Ha