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What is the meaning of the minLrap and maxLrap values ?

These values are ratios of alignment lengths computed for each comparison using the BLAST software :

  • minLrap = Lmatch/min(Lprot1, Lprot2)
  • maxLrap = Lmatch/max(Lprot1, Lprot2)

where Lmatch = length of the match, Lprot1 = length of protein 1, Lprot2 = length of protein 2.

if minLrap=1 and maxLrap=1 => the 2 proteins both align on their whole length

if minLrap=1 ans maxLrap<1 => one of the proteins is longer than the other, or the alignment is partial. Different interpretations are possible:

  • the longer protein is a modular protein (domain fusion/fission)
  • there is an erroneous start codon for one of the 2 genes
  • the smaller gene is a fragment (pseudogene).
  • a frameshift (due to a sequencing error or not) causes a premature stop codon in one of the genes.

if minLrap<1 and maxLrap<1 => the sequences are poorly aligned. We can observe this kind of situation in the case of gene remnants.

What is the meaning of orderQ and orderB values ?

The orderQ and orderB values give an information about the rank of the BLAST hit for a protein of the query genome (orderQ) or for a protein of a databank (orderB).

Best bidirectional Best Hits (BBH) will have a 1:1 relationship The following Best hits will have 1<=>n relationship

(PNG)

Tips: These indicators can be useful to identify fusion/fission events.