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Evolutionary Relationships Between Gene Sequences via Nonlinear
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FDUNOÕ DQDOL] SDUDPHWUHOHULQLQ GHQHQLS EX SDUDPHWUHOHULQ
RSWLPL]H HGLOPH\H oDOÕúÕOGÕ÷Õ DUDúWÕUPDGD ED]Õ SURWHLQ
ailelerinin fonksiyonel oODUDN ELUELULQH \DNÕQ \HOHULQLQ
evrimsel anlamda uzak SURWHLQOHUGHQ D\UÕOÕS iki boyutlu
uzayda gruplaQPDVÕ EDúDUÕOPÕú EX úHNLOGH GR÷UXVDO ROPD\DQ
J|PPH WHNQLNOHULQLQ SURWHLQ YH JHQ GL]LOHULQL NPHOH\HELOPH
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\|QWHPH H÷UL \]H\OHU ]HULQH GD÷ÕOPÕú YHULOHUL ELOH EDúDUÕOÕ
úHNLOGH \DNDODPD EHFHULVLQL ND]DQGÕUÕU $QDOL]H JLUGL RODUDN
YHULOHQ oÕNDUÕPVDQPÕú HYULPVHO X]DNOÕNODU NRPúX \DNÕQ
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noktalar DUDVÕQGDQ ELUoRN NoN DWODPD VW VWH HNOHQHUHN
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NXOODQÕODUDN X\JXODQPÕú RODQ GR÷UXVDO ROPD\DQ J|PPH
VRQUDVÕ HOGH HGLOHQ HYULPVHO X]DNOÕNODUÕQÕQ KDWD DQDOL]L
VXQXOPXúWXU %X UDSRUXQ VÕUDGDNL NÕVPÕQGD IDUNOÕ HYULPVHO
\ROODU L]OH\HQ VHQWHWLN GL]LOHULQ UHWLOPHVL YH KDWD DQDOL]LQLQ
JHUoHNOHúWLULOPHVL LoLQ NXOODQÕODQ SDUDPHWUH DoÕNODQPÕú WDNLS
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\D]ÕOÕPÕNXOODQÕODUDN\DSÕOPÕúWÕU
2.1. 6HQWHWLNJHQGL]LOHULQLQROXúWXUXOPDVÕ
6HQWHWLN JHQ GL]LOHULQLQ KD]ÕUODQPDVÕQGD o D\UÕ HYULPVHO \RO
L]OHQPLú DQDlizler de EX o \RO LoLQ D\UÕ D\UÕ
JHUoHNOHúWLULOPLúWLU (YULPVHO \ROODU RULMLQDO VHQWHWLN JHQ
GL]LVLQLQ ED]Õ E|OJHOHULQGH UDVWODQWÕVDO ED]DO \HU GH÷LúWLUPHOHU
\HUOHúWLULOPHVL LOH \HQL GL]LOHU ROXúWXUXOPDVÕQD GD\DQÕU Bu
RSHUDV\RQLúOHPVHORUWDPGDVLPXOHHGLOPLúWLU
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ROXúDQ\HQLGL]LOHURULMLQDO(ilk) GL]LGHQJLWWLNoHIDUNOÕODúÕUODU
Her bir evrimsel yolda 501¶HU (orijinal diziyle beraber) dizi
bulunur. +HU ELU GL]L QNOHRWLGGHQ ROXúXU $QDOL]GH
NXOODQÕODQ \HU GH÷LúWLUPH KÕ]Õ ¶GLU 'L÷HU ELU GH\LúOH YDU
RODQELUGL]LGHQ\HQLELUGL]LROXúWXUXOXUNHQGL]Llerde yer alan
YHKHUELULQLELUQNOHRWLGLQNDSODGÕ÷ÕE|OJHGHQKHUELUL
ioLQ eski dizideki QNOHRWLGLQ D\QHQ \HQL GL]L\H \HUOHúWLULOPH
ihtimali UDVWJHOH RODUDN IDUNOÕ QNOHRWLGGHQ ELULQLQ
\HUOHúWLULOPH LKWLPDOL LVH ¶GLU Evrimsel yol 1 (EY1),
Evrimsel yol 2 (EY2) ve Evrimsel yol 3¶Q (EY3)
olXúWXUXOPDVÕQGDL]OHQHQ\ROlar ùHNLO¶GHYHULOPLúWLU
HDWD GH÷HUOHUL (
øOLúNLOHUL
Evolutionary Relationships Between Gene Sequences via Nonlinear
Embedding
7XQFD'R÷DQ1%LOJH.DUDoDOÕ 2
1. %L\RWHNQRORMLYH%L\RPKHQGLVOLN %|OP,
ø]PLU0].
FDUNOÕ DQDOL] SDUDPHWUHOHULQLQ GHQHQLS EX SDUDPHWUHOHULQ
RSWLPL]H HGLOPH\H oDOÕúÕOGÕ÷Õ DUDúWÕUPDGD ED]Õ SURWHLQ
ailelerinin fonksiyonel oODUDN ELUELULQH \DNÕQ \HOHULQLQ
evrimsel anlamda uzak SURWHLQOHUGHQ D\UÕOÕS iki boyutlu
uzayda gruplaQPDVÕ EDúDUÕOPÕú EX úHNLOGH GR÷UXVDO ROPD\DQ
J|PPH WHNQLNOHULQLQ SURWHLQ YH JHQ GL]LOHULQL NPHOH\HELOPH
becerisi ortaya koyulPXúWXU>0].
ø]RPHWULN|]HOOLNKaritalama (ISOMAP)GR÷UXVDOROPD\DQ
J|PPH \|QWHPOHULQGHQ ELULGLU %X \|QWHP NODVLN
|OoHNOHQGLUPH LoLQH J|POPú RODUDN, NRPúXOXN GL\DJUDPÕ
]HULQGHNL MHRGH]LN X]DNOÕNODUÕ GLNNDWH DOÕU [6@ %X |]HOOLN
\|QWHPH H÷UL \]H\OHU ]HULQH GD÷ÕOPÕú YHULOHUL ELOH EDúDUÕOÕ
úHNLOGH \DNDODPD EHFHULVLQL ND]DQGÕUÕU $QDOL]H JLUGL RODUDN
YHULOHQ oÕNDUÕPVDQPÕú HYULPVHO X]DNOÕNODU NRPúX \DNÕQ
QRNWDODUDUDVÕQGDNLMHRGH]LNX]DNOÕNODUÕKHVDSODPDNLoLQiyi bir
\DNODúÕP RODUDN \HU DOÕU >6@ 8]DN QRNWDODU LoLQVH EX NRPúX
noktalar DUDVÕQGDQ ELUoRN NoN DWODPD VW VWH HNOHQHUHN
MHRGH]LNX]DNOÕNODUKHVDSODQDELOLU
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VRQUDVÕ HOGH HGLOHQ HYULPVHO X]DNOÕNODUÕQÕQ KDWD DQDOL]L
VXQXOPXúWXU %X UDSRUXQ VÕUDGDNL NÕVPÕQGD IDUNOÕ HYULPVHO
\ROODU L]OH\HQ VHQWHWLN GL]LOHULQ UHWLOPHVL YH KDWD DQDOL]LQLQ
JHUoHNOHúWLULOPHVL LoLQ NXOODQÕODQ SDUDPHWUH DoÕNODQPÕú WDNLS
HGHQE|OPGHLVHVRQXoODURUWD\DNRQXOPXúYH EX VRQXoODUÕQ
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2.1. 6HQWHWLNJHQGL]LOHULQLQROXúWXUXOPDVÕ
6HQWHWLN JHQ GL]LOHULQLQ KD]ÕUODQPDVÕQGD o D\UÕ HYULPVHO \RO
L]OHQPLú DQDlizler de EX o \RO LoLQ D\UÕ D\UÕ
JHUoHNOHúWLULOPLúWLU (YULPVHO \ROODU RULMLQDO VHQWHWLN JHQ
GL]LVLQLQ ED]Õ E|OJHOHULQGH UDVWODQWÕVDO ED]DO \HU GH÷LúWLUPHOHU
\HUOHúWLULOPHVL LOH \HQL GL]LOHU ROXúWXUXOPDVÕQD GD\DQÕU Bu
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ROXúDQ\HQLGL]LOHURULMLQDO(ilk) GL]LGHQJLWWLNoHIDUNOÕODúÕUODU
Her bir evrimsel yolda 501¶HU (orijinal diziyle beraber) dizi
bulunur. +HU ELU GL]L QNOHRWLGGHQ ROXúXU $QDOL]GH
NXOODQÕODQ \HU GH÷LúWLUPH KÕ]Õ ¶GLU 'L÷HU ELU GH\LúOH YDU
RODQELUGL]LGHQ\HQLELUGL]LROXúWXUXOXUNHQGL]Llerde yer alan
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ioLQ eski dizideki QNOHRWLGLQ D\QHQ \HQL GL]L\H \HUOHúWLULOPH
ihtimali UDVWJHOH RODUDN IDUNOÕ QNOHRWLGGHQ ELULQLQ
\HUOHúWLULOPH LKWLPDOL LVH ¶GLU Evrimsel yol 1 (EY1),
Evrimsel yol 2 (EY2) ve Evrimsel yol 3¶Q (EY3)
olXúWXUXOPDVÕQGDL]OHQHQ\ROlar ùHNLO¶GHYHULOPLúWLU
HDWD GH÷HUOHUL (