so what is this faster remember I told
you faster is another very popular
similarity Search tool Okay so
fast all capital like blast is also
similarity Search tool and in this case
also we have a query sequence
we call it
so word you know word every single
matching word
the matching word
the matching word will be known as
what let me write it down
k tuples
catapults
okay that is the matching word K tuples
as neighbor word in the blast we call it
as a in case of blast whenever the word
is matching we call them Neighbors in
case of faster if we are choosing word
which is matching we call it K2 plus
okay
now in this case the first algorithm is
actually developed by Lipman and Pearson
Lipman and Pearson founded this and
formed this algorithm
and in this case for a protein sequence
what is the length that we take in query
one to two amino acid long
for nucleotide sequence we choose 5 to 6
nucleotides so compared to blast it's
smaller in case of blast nucleotide is
now in this case words match with the
database sequence and creates diagonals
so in this case the faster uses Dot Plot
remember the Dot Plot if you recall the
Dot Plot they will understand what I
mean if you don't recall Dot Plot and if
you haven't seen my video on Dot Plot
please watch that video otherwise you
cannot understand this okay
so what it happens exactly if there is a
match then the Dot Plot is created based
on the match we what we do in the dot
plots we have this x and y axis and
there is match there is match there is
match what we if you draw a straight
line and no there is no match again a
match here so there is another straight
line so based on the Dot Plot we have
what we have this sequence a in x axis
will have sequence B in the y axis this
is what we'll have in the Dot Plot here
okay
this is how it's done
there are four steps in the process of
faster okay so first is a we search for
identical region among the query and the
database sequence
identical
region what we do we do a
search
of identical region the second thing
so whenever we find The Identical region
they are scored
this code with time Matrix
now there are scoring system in
bioinformatics there are two systems
used spam Matrix and Blossom Matrix so
again you need to know what is Spam
Matrix and Blossom Matrix how the
scoring system works you can watch my
video on that the portion of lecture on
that then you can understand blast uses
Blossom 62 but faster uses spam Matrix
so the scoring is done
and the best score is kept aside
okay best core is kept aside
then what else we have
segments
are joined
by Gap and such gapped alignment score
is known as
okay
so what we'll do
the blanks
joined
banks will be joined by the Gap
and we get a gap alignment score
gapped alignment score which is not so
because if this 100 similarity we get a
maximum score but we know that if there
is no hundred percent similarity the
score will be lesser than the maximum so
whatever value if the Gap is increasing
in Number the score values also decrease
Gap score value yeah Gap score value if
you consider the Gap the number of Gap
into the value then it will increase but
actually
if there is a gap then the matching
value number is decreasing
okay and then what we do we put an
algorithm known as meat Waterman
algorithm of local alignment
based on dynamic programming is used to
find out the optimal alignment so
ultimately use a look