<s>
The	O
Shapiro	B-Algorithm
Senapathy	I-Algorithm
algorithm	I-Algorithm
(	O
S&S	O
)	O
is	O
an	O
algorithm	O
for	O
predicting	O
splice	O
junctions	O
in	O
genes	O
of	O
animals	O
and	O
plants	O
.	O
</s>
<s>
Using	O
a	O
weighted	O
table	O
of	O
nucleotide	O
frequencies	O
,	O
the	O
S&S	O
algorithm	O
outputs	O
a	O
consensus-based	O
percentage	O
for	O
the	O
possibility	O
of	O
the	O
window	O
containing	O
a	O
splice	O
site	O
.	O
</s>
<s>
The	O
Shapiro	B-Algorithm
–	I-Algorithm
Senapathy	I-Algorithm
algorithm	I-Algorithm
has	O
been	O
used	O
to	O
discover	O
genes	O
and	O
mutations	O
involved	O
in	O
many	O
immune	O
disorder	O
diseases	O
,	O
including	O
Ataxia	O
telangiectasia	O
,	O
B-cell	O
defects	O
,	O
epidermolysis	O
bullosa	O
,	O
and	O
X-linked	O
agammaglobulinemia	O
.	O
</s>
<s>
The	O
Shapiro	B-Algorithm
–	I-Algorithm
Senapathy	I-Algorithm
algorithm	I-Algorithm
has	O
been	O
used	O
to	O
determine	O
the	O
various	O
aberrant	O
splicing	O
mechanisms	O
in	O
genes	O
due	O
to	O
deleterious	O
mutations	O
in	O
the	O
splice	O
sites	O
,	O
which	O
cause	O
numerous	O
diseases	O
.	O
</s>
<s>
The	O
proper	O
identification	O
of	O
splice	O
sites	O
has	O
to	O
be	O
highly	O
precise	O
as	O
the	O
consensus	B-Operating_System
splice	O
sequences	O
are	O
very	O
short	O
and	O
there	O
are	O
many	O
other	O
sequences	O
similar	O
to	O
the	O
authentic	O
splice	O
sites	O
within	O
gene	O
sequences	O
,	O
which	O
are	O
known	O
as	O
cryptic	O
,	O
non-canonical	O
,	O
or	O
pseudo	O
splice	O
sites	O
.	O
</s>
<s>
Shapiro	B-Algorithm
–	I-Algorithm
Senapathy	I-Algorithm
algorithm	I-Algorithm
can	O
identify	O
the	O
cryptic	O
splice	O
sites	O
,	O
in	O
addition	O
to	O
the	O
authentic	O
splice	O
sites	O
.	O
</s>
<s>
The	O
intron-exon	O
boundaries	O
of	O
Sf9	O
fut8	O
were	O
in	O
agreement	O
with	O
the	O
consensus	B-Operating_System
sequence	O
for	O
the	O
splicing	O
donor	O
and	O
acceptor	O
sites	O
concluded	O
using	O
S&S	O
.	O
</s>
<s>
In	O
fact	O
,	O
these	O
stop	O
codons	O
were	O
found	O
to	O
form	O
the	O
“	O
canonical	O
”	O
AG:GT	O
splicing	O
sequence	O
,	O
with	O
the	O
three	O
stop	O
codons	O
occurring	O
as	O
part	O
of	O
the	O
strong	O
consensus	B-Operating_System
signals	O
.	O
</s>
<s>
These	O
stop	O
codons	O
are	O
shown	O
in	O
the	O
consensus	B-Operating_System
canonical	O
donor	O
splice	O
junction	O
as	O
AG:GT	O
(	O
A/G	O
)	O
GGT	O
,	O
wherein	O
the	O
TAA	O
and	O
TGA	O
are	O
the	O
stop	O
codons	O
,	O
and	O
the	O
additional	O
TAG	O
is	O
also	O
present	O
at	O
this	O
position	O
.	O
</s>
<s>
These	O
consensus	B-Operating_System
sequence	O
clearly	O
show	O
the	O
presence	O
of	O
the	O
stop	O
codons	O
at	O
the	O
ends	O
of	O
introns	O
bordering	O
the	O
exons	O
in	O
all	O
eukaryotic	O
genes	O
.	O
</s>
<s>
Dr.	O
Senapathy	O
wanted	O
to	O
detect	O
the	O
splice	O
junctions	O
in	O
random	O
DNA	O
based	O
on	O
the	O
consensus	B-Operating_System
splice	O
signal	O
sequences	O
,	O
as	O
he	O
found	O
that	O
there	O
were	O
many	O
sequences	O
resembling	O
splice	O
sites	O
that	O
were	O
not	O
the	O
real	O
splice	O
sites	O
within	O
genes	O
.	O
</s>
<s>
The	O
stop	O
codons	O
within	O
splice	O
junctions	O
turned	O
out	O
to	O
be	O
the	O
strongest	O
bases	O
in	O
splice	O
junctions	O
of	O
eukaryotic	O
genes	O
,	O
when	O
tested	O
using	O
the	O
PWMs	O
of	O
the	O
consensus	B-Operating_System
sequences	O
.	O
</s>
