MicroScope Platform Overview
- Overview of the annotation editor
- Annotation Rules
- BLAST results
- Compositional features
- E. coli K12
- B. subtilis
- MaGe/Curated annotations
- Syntonome / Syntonome RefSeq
- Similarities SwissProt / TrEMBL
- Predicted MetaCyc Pathways
MicroScope - Tutorial » MaGe » Gene Annotation Editor » BLAST results
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 :
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:
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
Tips: These indicators can be useful to identify fusion/fission events.