of identification method to a phylogenetic group :
The program compares the query nucleotide
sequence(s) from panC gene to sequences in a database, in multiple steps,
and calculates the % homology and the statistical significance of matches
with all database sequences. The phylogenetic group containing the sequence
for which the homology is the highest is selected.
• The sequences AACAAAC or
AACAGAC are needed to initiate alignments, so that one of theses two initial
sequences must be present on the query sequence(s). The program then extends
alignment to generate the final alignment.
• Length of query sequence(s) must be over than 250 bases.
Mathematic formula for
% homology calculations and significance of matches :
The program calculates the percentage
of homology, from initial sequence (AACAAAC or AACAGAC) to the end of
the alignment (end of the database sequence or end of the query sequence
if it is shorter than the database sequence).
* number of bases covering the alignment
When the highest % homology is < 90%, identification
to phylogenetic groups is considered as not significant and rejected.
When the highest % homology is <75%, identification to the B. cereus
Group is considered as not significant and rejected.