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~ BEL 41f? tJo.5

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#!/usr/local/bin/perl
sw.pl
~.~
#Smith-Waterman Algorithm

# Requires two command line arguments

#Inputs in the form seql and seq2
#Inputs in the form seql and seq2
printfCftEnter sequencel:");
$seql = <>;
printfCft\nEnter sequence2:");
$seq2 = <>;
$lenl = length(Sseql);
$len2 = lengthCSseq2);

#Initialize firit row and column with multiples of gap penalty

$gp=O;
forC$i=O;Si<=$len2;$i++)
{
$table[O][Si] = $gp*$i;
}
for($j=O;Sj<=Slenl;$j++)
{ . .
$table[$j][O] = $ gp*$ J;
}

$gp=-l; #Gap pena hy

#Coopfor \1&i,n~ t:hr~ugh each

forC$i=l;$l<=$ienl;$i++)
{ ,
entry
- -- -- - -- --
forC$j=1;$j<=$len2;$j++)
{ .
#Calculate match bonus or mlsmatch penalty
$mb=l;
$misp=-l;
$a=substr($seql,$i-l,l);
$b=substr($seq2,Sj-l,1);
if (Sa eq $b)
{
$match= $mb;

}
else
{
$match=$misp;
}

my $l=$table[$i] [$j-l]+$gp; #From left

my $r=$table[$i-l]l$j]+$gp; #From above
my $d=$table[$i-l] [$j-l] + $match; #From Diagonal
#compute maximum of three values
if(C$l>$r) && C$l>$d))
{
$table[$i] [$j]=$l;
$arrow[$i] [$J] =ft rft;
}
elsif«$r>$l) && ($r>$d))
Page 1
 The experiment paradigm used for the present study is function has the form of a sum of square (as is typical in
similar to an earlier researeh done in our laboratory training feed forward network). then the Hessian matri.\
r10]. The subject was asked to comfortably lie down can be approximate as H=JTJ and gradient can be
in a relaxed position Ilith eyes closed- Initiall~ the computed as g=.ITe.Were J is the jacobian matrix that
subject was asked to relax II)r 5 min- Alier assuring contains first derivatives of the network errors \\ith
the normal relaxed state by checking the status of the respect to the weights and biases, and e is a vector of
alpha waves. the EEG I\-asrecorded fl)r ::.session of 5
s epoch each for relaxed state- This is used as basic net\\ork errors. The Levenberg-Marquardt algorithm
uses this approximation to the Hessian matri:..:in the
n:ferenee for further analysis of the planning data. The ttJIIO\\-ingNewton-like update:
subject was asked to mentally plan to mO\-e the right
handed thumb. on presentation of an audio eue. both at
Xk+l=X,,_pTJ+/-IIJ,1 JT e
the start and cnd of a session- 5 sessil)fJ of each
planning and relaxed data were reeorded each with a
time gap of 180s .The I\-hole e:\periment including a... aff"""'~.
preparation of the subjects last flJI' I hr. collecting
EEG data II)r the, 5 sessions- The 5s epochs related
normal rel<L"\edand planning period were first pruned
for artifacts and then analyzed as the foJlml"ingsetting
high pass lilter 5Hz and loIVpass tilter 1.6 Hz. notch
lilter 50 Hz .sensitivity 70 IIvfml11and a sampling rate
of 256-

As the first step. Frequency spectrum of the signal was

analyzed with FFT plots. The FFT plots IVere
observed to compare changes in mu activity during
relaxcd state and movement imagery - The peaks for
C3 & C4 almost coincide in alpha band (7-13 Hz) at a ~~

particular base frequency for relaxed st2.te.~\\Jlj..!ea. ~

maximum of 500/o...band '-Power ath:nuation was
~ observed in C3 IV.r.t.C4 (I)r movement imagery. at the
same base frequency. [11-121- The data was further
processed using Wavelet packet transt()fm to extract
the most relevant feature vector froln the signal which -.
could bccome a base vector II)r the dassitication of
the two stages'I3-14J. Walekt codtieients are used
as the ifp vector for ANN. Fig 2 -Architecture of ANN

8. .-frlljicial Neural Net1\'ork

The main advantage of choosing the neural network
1()r classitieation of such data is that ANN-s can be
used to soh-e difficult problem. \I-here description I()r
the data is not computable. ANN can be trained using
example to discriminate the realu.-e II)r analysis wc
ha\-e used the mat lab \-et"sion 7 II)r the analysis-
Topology specit~- the neural net\lork architectUre in
Figure21J5-171
Follo\\ing is a desniption of thc methods
this im-estigation
When the scalar /-Iis zero, this is just Newton -s method-
using the appro:..:imate Hessian matrix- When ~l is large.
this hecomes gradient descent with a small step size-
NewlUn-s method is faster and more accurate near an
crror minimum. so the aim is to shift to\\ard Ne\1 tOll-s
method as quickly as possible. Thus. ~I is decreased
alkr each successful step (reduction in perll)ffllanCe
fUllction) and is increased only whcn a tentatile step
Ilouid increase the performance function- In Ihis \\ a~,
the pertl)ffl1anCe function is always reduced at each
iteratioll of the algorithm. Thc value of training
used in p<lr<lmetersII)r present study given in table 1-

('. I.(,J"<!/Iberg- lIul"<l/I,-<l1

rhe Ie\enherg -l\larquardt algorillull \\ as design to

approach second ordn training 'pced II ithoul hal ing
to cnmpule the I k,sian m~i!ri_'\-\\he'll Ih\' perll)l"Illanee

~"
- ",....-----
 SW.pl
{
$table[$i] [$jJ=$r;
Sarrow[$i] [$j]="u";
}
# elsif«$d>$r) && ($d>$l))
else
{
$table[$i] [$j]=$d;
$arrow[$i] [$j]="d";
}
#If resulting value<O, make it zero.
i f($tab 1 e [$i J [$j] <0)
{
$table[$i] [$j]=O;
}
}
}
$max=O;
#Display table and find maximum entry value
for($i=O;$i<=$lenl;$i++)
{
for($j=0;$j<=$len2;$j++)
{
pri ntf("Stab 1 e [$i] [$j] \ t") ; #For displaying the table

if($table[$i] [$j]>$max) #For finding Maximmum value

{ $i1=$i;
$j2=Sj;
$max=Stable[$i] [$j];
}
} -
printf("\n");
} .
printf("Maximum value is $max\n");

#For finding the alignment

$len=O;
#LOOp till substring of max length is found.
for(Si=Sil;(Si>O) && (Smax>O);)
{
for(Sj=$j2; (Sj>O) && (Stable[Si][$j]!=O) && ($max>O);)
{ #printf("loop");
#printf("$arrow[$i] [$j]\n");

$x=$arrow[$i] [$j];
if($x eq "d") #Go to diaconal element
{
$i--;
$j--;
$disl[$len]=substr($seql,$i,l);
$dis2[$len]=substr($seq2,$j,l);
}
elsif($x eq "U") #Go to above element
{
$i--;
$dis2[$len]="-";
$dis1[$len]=substr($seql,Si,l);
}
#elsif($x eq "r") #Go to left element

page 2
 Pa 1">1
JlwtCI' Valuc
1\1;11..grad 1e.5 nctwork classifier to classify planlJing of right hand
_.- movement and relaxed state. For the present stucl~
Epoch 5000
Lev.:nberg-Marquardt showed better compare to RBI'.
I\lu 0001
--- Figure 3 showed eomparisolJ of classitication accurac~
!\lu dee 01 for LM and RBI' methods
!\Ill..ine 10
Gn1 Classification Accuracv (%)
Ie.O6
Session Le\'enberg- Radial basis
'"krn redue
marquard! function
!\1, Mu I 1e10 I 78.84 75.00
T~hlc I Dirferent valuc ofparanl<'I<'r 2 75.00 7058
3 6703 66.66
D. Radia! basis jill1cliol1l1cllI'(wk 4 65.384 6315
5 63.46 60,00
A typical RBI' Iletworks consist of three layer of Average 69.94 67.07
-
neuron (input. hiddell. output) which arc compollenl of T~ble2; colt)p~rison of accuracy ofLM&RBF method
fuUy connccted feed forwurd archita:ture. The special
IV. DISCUSSION AND CONCLUStON
radial b1Jj;;SbLl~avior is performed hy the single layer
of hidden neurons. The activation of a hiddcn neuron
is dcterrnined in 1\\0 steps. The !irs! js cOl11puti"~gthe The present studies evaluate tlte performance of t\\'o
distance '(USU,ll!y by using the Euclidean norm). ANN methods. We compared the perfonnance of
hetween tl1\; two veclOrs which arc yielding by the n.:uralnctwork (NN) method Levenbcrg-Mnrquardt and
activation of the input layer (x) and th.: link IV.:ight Radial basis function netwQrk for planning of right hand
between the input layer and the current hidd.:n layer, movement w,r.t. relaxed state. Levenberg-Marquardt
second n function h which is bcll shaped (c.g. method showed the highest penormance with the
Gaussian) is applied. using the obtained distance to accuracy 01'78.8%.
"
get the Uilitl activation of the hidden neuron. The
~H;tjvation of ;ll1euron in the ()utputla~..;r is t1Clcnnincd
liS usual h~ C{}11-1pm:ing "tile w.:ighted sum ofinpul.
Radii\1 basis \\"(}rkbest when many training \.:ctors ar.:
available. A RBI' network can be described as a linear
combination of basis function i.c. 8° -.'I---;
~,..60
" r
.'-==~~~j::~7~"r;;;:
~ I
/. 0"0.f(xl'~ ~ 0,11>, (x) ~ 401
Whae
=;: /? Ihe output variab!.:: j i
X): I? thc input variable: ~20
G
(I, the optimal \\'.:ight~:
</'(.\"I the radial basis functiolJ. oL
3
Session

Fig 3-classilicatio accuracy Ii>.'I.M and RBI'

There arc m"l1~ choicc~ II)r thi: radial ba~i~ function.
\\' I.'~el.:ct<.:dth\.' (iaussiall fu11\.'tion defined as
Aft\.'r successfully discriminating the t\\'o cognith\.'
stales as awak.: relaxed and a planning of right hand
-'x - x, mOlelllent. Wavelet packct transform used to <':xlractth,~
l1lo~1 rele\ant feature vector from the signal which
<P.(.\" I '"' ('.IP.( 2cr:' ) could b\.'coille a base vector for th\.' classification of the
I 1\0 ~tages. /\ comparison 1\as made b\.'ll\ \.'\.'n
rhe parall1c't.;r ," cOIJII"OI~;
Ihe radius of jnllu\.'nc\.' of 1.\.'\'\.'llberg-l'vlarquardt and Radial basis fUllction

":.11.'11hasi, t"lIIJC!jOIl. ,111<1.1, rl'j'r\.'s\.'nlS its c\.'lller IIX- 1l\.'lllork. Wher\.' the perfi.)f"Jnance giv<.:n b~ Le\ \.'nberg-
191, \Iarquardt method i~ signilicantly bett\.'r than oth<:r.

III RESUL T

1,lble :2 sholl Ihl' L"lll!',lli,olJ of the p,'rl('nndllcc of

I 1.'1,'lJh,'I'!: - \ l"re!lI,II<lt 8: Radial ha,j, (lIIlCI jplJ
 ACKNOWLEDMENT
Thc author's acknO\lkdge Iheir gratitude tOIlard,
math \lorks for \I alekt alld Ileural Ilct\lork tooll1o.\
\\hich helpcd 10 compik Ihe result.
REFERENCE
III .I.R.Wolpa". NBirbaumer. I)) Mc Farland. G.Plurtschelkr.
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'No
[31 .lR Wolp"". TlVLVaughan and E.Dunchin. "U..:(; Ba,,'d
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Trans. Rehah.J:ng,,\OIA..ppA25--I30, Dec. 1996.
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EEG/EMG dynamic Synchronous and desynchronous basic
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1999.
['II .I R \\','Ipa\\. D. J. Me Far!and. T 1\1 Vaughan. 'Ihe \lads
'\l>rtP Cemre Brain l'omp'Her inler!;,ee leseareh and
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,ehab Eng" 1112))20-l..207.200}
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C"gllni\e braill fl'search 22.59..66. 20()-I.
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\'('mpllter inlert",e ill mullimedia rommllllleation."IEEE
SIgnal rrneessing magazine. 1-1/20.2000.
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"~epalabihly o!" EEG signals recorded dllring roght and :en
n"'tor imagen' using adaptive allto regre<.SI\e parameters:'
liTE. Tmns. on rehabilitation Ellgineering. fl..:;. rp316..3~5
1"9~.
11.~I \1 Aka\. Walelet in biomedICal en!,lnwrilig. allnatsin
Ih,'medkal Engineering, 23 (5). 5:; 1..~-I2.IW~
11-11 Ci,lI",rt Strallg and Troung Ngllgen. Wa\elel and Ftll<r E5ar.ks
\\'dksley.Cambridge pre;s, 1997.
II ~I 1\c'ural N':lwork toolbox. Ihe math works Inc 1998.
1161 S.lIa\ kin Neural Net\\'ork.. /\ Comprehensi\\.' t.'undatim). 2""
FJmon .Prentice Ilall, 2000.
[171 i\t Hag"n. II Demuth. and M. beale. Nellral Nel\\'ork dcsign
H,'slt'n MA.. PWS Publishing. 1996.
I!XI K. Warwick. J!\hlson" arKIESutanto., "Centre Selection lor
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IllJl
31)<J:3 11. . -
...\ks. France ,D. l'earsnn.N.Sc'Ctlc and R Albr.:ehl(Eos)
~- -~ ~
S.l'hcn. . C.F.N. Cowan, and P. M Grant.""'i)nh,~JOri'i!ILeasl
S..;",!!,;, Learning Algnrithnl for Radial Oasis runction
N~l\\t)fks." IEEE Transactions on Nellral Networks, \'tll. 2. n<l.
2. pp. 301..3()<).March 19'11. 1995.
 -~
~
sw.pl
else
{
$j--;
$disl[$lenJ="-";
$dis2[$lenJ=substr($seq2,$j,1);
}
$len++;
$max--;
}
}

#Display, the alignment.

printf('Alignment\n");
for($z=$len;$z>=O;$z--)
{
printf("$disl[$z]");
}
pri ntf("\n").;
for($z=$len;$z>=O;$z--)
{
printf("$dis2[$z]");
}
<STDIN>;

.~ -=-
=~~
=-=-. ""' = = =="'" ~".~
'"
""

Page 3