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<div class="document" id="last-built-in-scoring-schemes">
<h1 class="title">LAST built-in scoring schemes</h1>
<div class="section" id="at77">
<h2>AT77</h2>
<p>This scoring scheme is for weakly-similar AT-rich DNA (~27%
substitutions and ~77% A+T) (MC Frith, NAR 2011 39(4):e23).
It uses this matrix:</p>
<pre class="literal-block">
A C G T
A 2 -3 -2 -3
C -3 5 -3 -2
G -2 -3 5 -3
T -3 -2 -3 2
</pre>
<p>It sets these default lastal parameter values:
-a15 -b2</p>
</div>
<div class="section" id="atmap">
<h2>ATMAP</h2>
<p>This scoring scheme is for strongly-similar AT-rich DNA (~4%
substitutions and ~76% A+T). It is also suitable for sequences with
more than 4% substitution errors, if the excess error rate is
explained by quality scores.
It uses this matrix:</p>
<pre class="literal-block">
A C G T
A 4 -12 -12 -12
C -12 9 -12 -12
G -12 -12 9 -12
T -12 -12 -12 4
</pre>
<p>It sets these default lastal parameter values:
-a24 -b6</p>
</div>
<div class="section" id="bisf">
<h2>BISF</h2>
<p>This scoring scheme is for aligning bisulfite-converted DNA forward
strands to a closely-related genome (MC Frith, R Mori, K Asai, NAR
2012 40(13):e100).
It uses this matrix:</p>
<pre class="literal-block">
A C G T
A 6 -18 -18 -18
C -18 6 -18 3
G -18 -18 6 -18
T -18 -18 -18 3
</pre>
<p>It sets these default lastal parameter values:
-a21 -b9</p>
</div>
<div class="section" id="bisr">
<h2>BISR</h2>
<p>This scoring scheme is for aligning bisulfite-converted DNA reverse
strands to a closely-related genome (MC Frith, R Mori, K Asai, NAR
2012 40(13):e100).
It uses this matrix:</p>
<pre class="literal-block">
A C G T
A 3 -18 -18 -18
C -18 6 -18 -18
G 3 -18 6 -18
T -18 -18 -18 6
</pre>
<p>It sets these default lastal parameter values:
-a21 -b9</p>
</div>
<div class="section" id="bl62-or-blosum62">
<h2>BL62 or BLOSUM62</h2>
<p>This protein scoring scheme is quite good at finding long-and-weak
similarities, and not terrible at short-and-strong similarities (S
Henikoff & JG Henikoff, PNAS 1992 89(22):10915-9).
It uses this matrix:</p>
<pre class="literal-block">
A R N D C Q E G H I L K M F P S T W Y V B J Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -1 -4
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2 0 -1 -4
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 -3 0 -1 -4
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 -3 1 -1 -4
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 -2 4 -1 -4
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 -3 4 -1 -4
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -4
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 -3 0 -1 -4
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 3 -3 -1 -4
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 3 -3 -1 -4
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 -3 1 -1 -4
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 2 -1 -1 -4
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 0 -3 -1 -4
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 -2 0 -1 -4
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 -1 -1 -4
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -2 -2 -1 -4
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -1 -2 -1 -4
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 2 -2 -1 -4
B -2 -1 4 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 -3 0 -1 -4
J -1 -2 -3 -3 -1 -2 -3 -4 -3 3 3 -3 2 0 -3 -2 -1 -2 -1 2 -3 3 -3 -1 -4
Z -1 0 0 1 -3 4 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -2 -2 -2 0 -3 4 -1 -4
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
</pre>
</div>
<div class="section" id="bl80-or-blosum80">
<h2>BL80 or BLOSUM80</h2>
<p>This protein scoring scheme is good at finding somewhat
short-and-strong similarities. (S Henikoff & JG Henikoff, PNAS 1992
89(22):10915-9).
It uses this matrix:</p>
<pre class="literal-block">
A R N D C Q E G H I L K M F P S T W Y V B J Z X *
A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -6
R -2 6 -1 -2 -4 1 -1 -3 0 -3 -3 2 -2 -4 -2 -1 -1 -4 -3 -3 -1 -3 0 -1 -6
N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -4 5 -4 0 -1 -6
D -2 -2 1 6 -4 -1 1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4 5 -5 1 -1 -6
C -1 -4 -3 -4 9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -2 -4 -1 -6
Q -1 1 0 -1 -4 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -3 -2 -3 0 -3 4 -1 -6
E -1 -1 -1 1 -5 2 6 -3 0 -4 -4 1 -2 -4 -2 0 -1 -4 -3 -3 1 -4 5 -1 -6
G 0 -3 -1 -2 -4 -2 -3 6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -5 -3 -1 -6
H -2 0 0 -2 -4 1 0 -3 8 -4 -3 -1 -2 -2 -3 -1 -2 -3 2 -4 -1 -4 0 -1 -6
I -2 -3 -4 -4 -2 -3 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -4 3 -4 -1 -6
L -2 -3 -4 -5 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -2 1 -4 3 -3 -1 -6
K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 -1 -1 -4 -3 -3 -1 -3 1 -1 -6
M -1 -2 -3 -4 -2 0 -2 -4 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 2 -1 -1 -6
F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 0 6 -4 -3 -2 0 3 -1 -4 0 -4 -1 -6
P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4 8 -1 -2 -5 -4 -3 -2 -4 -2 -1 -6
S 1 -1 0 -1 -2 0 0 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -3 0 -1 -6
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2 1 5 -4 -2 0 -1 -1 -1 -1 -6
W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2 0 -5 -4 -4 11 2 -3 -5 -3 -3 -1 -6
Y -2 -3 -3 -4 -3 -2 -3 -4 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -3 -2 -3 -1 -6
V 0 -3 -4 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 2 -3 -1 -6
B -2 -1 5 5 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 5 -4 0 -1 -6
J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 3 -3 2 0 -4 -3 -1 -3 -2 2 -4 3 -3 -1 -6
Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -1 -4 -2 0 -1 -3 -3 -3 0 -3 5 -1 -6
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
</pre>
</div>
<div class="section" id="hoxd70">
<h2>HOXD70</h2>
<p>This scoring scheme is often used for weak DNA similarities (F
Chiaromonte, VB Yap, W Miller, PSB 2002:115-126).
It uses this matrix:</p>
<pre class="literal-block">
A C G T N
A 91 -114 -31 -123 -100
C -114 100 -125 -31 -100
G -31 -125 100 -114 -100
T -123 -31 -114 91 -100
N -100 -100 -100 -100 -100
</pre>
<p>It sets these default lastal parameter values:
-a400 -b30</p>
</div>
<div class="section" id="miqs">
<h2>MIQS</h2>
<p>This scoring scheme is for finding remote protein homologs (K Yamada
& K Tomii, Bioinformatics 2014 30(3):317-25).
It uses this matrix:</p>
<pre class="literal-block">
A R N D C Q E G H I L K M F P S T W Y V B J Z X *
A 3 -1 0 0 2 0 0 0 -1 -1 -1 -1 -1 -2 0 1 1 -4 -2 0 0 -1 0 -1 -6
R -1 6 0 -1 -3 2 -1 -2 1 -2 -3 3 -1 -3 -1 0 -1 -4 -2 -2 -1 -2 -1 -1 -6
N 0 0 5 3 -2 1 1 0 1 -4 -4 1 -2 -3 -1 1 0 -5 -1 -3 4 -4 1 -1 -6
D 0 -1 3 6 -4 1 3 -1 0 -5 -5 0 -3 -6 0 0 0 -5 -4 -3 5 -5 3 -1 -6
C 2 -3 -2 -4 12 -3 -3 -2 -1 0 -2 -3 0 -3 -3 1 0 -6 -1 2 -3 -1 -3 -1 -6
Q 0 2 1 1 -3 4 2 -2 1 -2 -2 2 0 -2 0 0 0 -5 -3 -2 1 -2 2 -1 -6
E 0 -1 1 3 -3 2 4 -1 0 -3 -3 1 -2 -4 0 0 0 -6 -2 -2 2 -3 4 -1 -6
G 0 -2 0 -1 -2 -2 -1 8 -2 -5 -5 -2 -4 -5 -2 0 -2 -5 -4 -4 -1 -5 -1 -1 -6
H -1 1 1 0 -1 1 0 -2 7 -2 -2 0 -2 0 -2 0 0 0 2 -2 0 -2 0 -1 -6
I -1 -2 -4 -5 0 -2 -3 -5 -2 5 3 -2 2 1 -4 -3 -1 -1 -1 3 -5 4 -3 -1 -6
L -1 -3 -4 -5 -2 -2 -3 -5 -2 3 5 -2 3 2 -3 -3 -2 0 0 2 -5 4 -3 -1 -6
K -1 3 1 0 -3 2 1 -2 0 -2 -2 4 -1 -4 0 0 0 -4 -2 -2 0 -2 1 -1 -6
M -1 -1 -2 -3 0 0 -2 -4 -2 2 3 -1 5 1 -3 -2 -1 -2 -1 1 -3 3 -2 -1 -6
F -2 -3 -3 -6 -3 -2 -4 -5 0 1 2 -4 1 7 -4 -3 -2 4 5 0 -5 2 -4 -1 -6
P 0 -1 -1 0 -3 0 0 -2 -2 -4 -3 0 -3 -4 8 0 0 -4 -5 -3 0 -3 0 -1 -6
S 1 0 1 0 1 0 0 0 0 -3 -3 0 -2 -3 0 3 2 -4 -2 -1 0 -3 0 -1 -6
T 1 -1 0 0 0 0 0 -2 0 -1 -2 0 -1 -2 0 2 4 -5 -2 0 0 -1 0 -1 -6
W -4 -4 -5 -5 -6 -5 -6 -5 0 -1 0 -4 -2 4 -4 -4 -5 15 5 -3 -5 0 -6 -1 -6
Y -2 -2 -1 -4 -1 -3 -2 -4 2 -1 0 -2 -1 5 -5 -2 -2 5 8 -1 -3 0 -2 -1 -6
V 0 -2 -3 -3 2 -2 -2 -4 -2 3 2 -2 1 0 -3 -1 0 -3 -1 4 -3 3 -2 -1 -6
B 0 -1 4 5 -3 1 2 -1 0 -5 -5 0 -3 -5 0 0 0 -5 -3 -3 5 -5 2 -1 -6
J -1 -2 -4 -5 -1 -2 -3 -5 -2 4 4 -2 3 2 -3 -3 -1 0 0 3 -5 4 -1 -1 -6
Z 0 -1 1 3 -3 2 4 -1 0 -3 -3 1 -2 -4 0 0 0 -6 -2 -2 2 -1 4 -1 -6
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6 -6
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
</pre>
<p>It sets these default lastal parameter values:
-a13 -b2</p>
</div>
<div class="section" id="pam30">
<h2>PAM30</h2>
<p>This protein scoring scheme is good for finding short-and-strong
similarities (MO Dayhoff et al. 1978).
It uses this matrix:</p>
<pre class="literal-block">
A R N D C Q E G H I L K M F P S T W Y V B J Z X *
A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -6 -3 -1 -17
R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -7 -4 -1 -17
N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -6 -3 -1 -17
D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 -10 1 -1 -17
C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -9 -14 -1 -17
Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 -5 6 -1 -17
E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 -7 6 -1 -17
G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -10 -5 -1 -17
H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -7 -1 -1 -17
I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 5 -6 -1 -17
L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 6 -7 -1 -17
K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -7 -4 -1 -17
M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 0 -5 -1 -17
F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -2 -13 -1 -17
P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -7 -4 -1 -17
S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -8 -5 -1 -17
T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -5 -6 -1 -17
W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -7 -14 -1 -17
Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -7 -9 -1 -17
V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 0 -6 -1 -17
B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 -8 0 -1 -17
J -6 -7 -6 -10 -9 -5 -7 -10 -7 5 6 -7 0 -2 -7 -8 -5 -7 -7 0 -8 6 -6 -1 -17
Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 -6 6 -1 -17
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -17
* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
</pre>
<p>It sets these default lastal parameter values:
-a13 -b3</p>
</div>
</div>
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