Optimal alignment
- alignment which gives the closest match, i.e. the smallest number
of differences
Two sequences which are to be compared may be of different
lengths, and the need to allow for deletions and insertions.
Polymorphism
Generally, a particular type of protein has the same, or a very similar
sequence within one species of organism. However there are cases of
polymorphism,
where several different functional sequences exist for a given type of
protein within the population.
50% identical sequences ¡Ú 50% homologous
Strictly, two sequences, or two subsequences, may be either homologous,
or they may be non-homologous; there are degrees
of similarity between sequences, but no degrees of homology.
During evolution, genes become cut, rearranged, joined together and duplicated.
As a result, proteins contain sections with homology to several other proteins.
Such a protein may be described as "partially homologous" to a number of
related structures.
EGF ----@----------@-@-@-@-----####-----@---@-@-@-@------
C9 ---f-f-------------------@----
LDL ---f-f-f-f-f-f-f-@-@---####-------@-
Low-density lipoprotein (LDL) receptor =>
34% of its DNA from an ancestral gene for
Complement component 9 (C9), 48%
from epidermal growth factor (EGF) and 18%
from elsewhere.
=> They are partial homologous.
LDL receptor are 34%
homologous to C9 and 48%
homologous to EGF.