vil) Transition Tronsvensien9 aligning —Nucleotices LBtA) Ltox NA) ch > +1 Mismatch -> +O Gap penalty >-1 ACHT LIGA TACG CC TATA a TOTALS, t, = tT HATO at-—-Are am TeTAT CT rad tht__Allgnment score? . 2 FX-1 (45> Align rant score = 184 0 =F = at foo. © Scove matrix tox fox aligning Amino_acid +— 2. eS : ty Pal ee an ii) BLossum/ Sere PAM s- 9 Paint Ere Mutahien based on ob) 9k was fxs given_by Aaya otobal auigh rant on ea re Sto chiensA Ke. H DB c as prety R a ds as _lene_percant)17._ cr isa enz__nuttahen pen _100_*. G é g 4 5 oe ae 7 4 PRN _suunabent. conmelase carl fy <7 PARA units and tu _evetutenatyr Re of Hat _proiein —sedpuennees. ' “a 2 jj for Bromple Pana motrix Senter: (4 140-260) tp ; Fi, es = Tr fy tc 1 es By 2 ¢ | Ve. ~ S r PAML= utatien even that change 17. of FE 3 ‘ ancine avid _t [ | % timitahen: of PAM. . - O_lestautien bared en tar phylogench' retlatien-—-—KNé hip priox_to coving nuttaden 3 a abe (ip of clutenmrining the anteshral, srelatien- = ship Cn eng, SectnnicLs. @. Bawden “a smac sce_ot dostly. -ubaded = oe moteins.. Seo (9) 9¢ drow diffeyrnre =t eox Hue _f A . ik ALR tia ee 4 K H ae ' 5-0-1 fi a eo 2 = uy iy ae Ss -4 y m 2 2 Ss -y 20° 45 ..-5 P eee sO fae ey SmI ie weg. 4 5 % boyholf PRM es CAraw it feooasenyt) : Point Mutation No mutation ae — Silent Morrunth n= eNAled TTC sere ATC nay Ry AAG. AAA. VAG Pate Ge: Qlagamn': Ht isa center of Block cumind cic! SEER oauhix. D_Benived on the bests of _cl’xect obse substi eutny. possible _anmino_acicl +t ; ; Sequance —_patterur__}s_also coulled cus cergapp volius od secpuner _setecteol far muha. @__BLosuM tensbictings Hee _racubae —is_cun of 27. @ Blossum Sequenct fox__q__pantitulart_resictuix pak duived fem te tog __natio_st _chsenved substitution _vevus “dhe expected probability cb dhe ondiculan —satatelue . Rewer the mumbe_of _ Blosscun > more _ cli vesagent Species anc present. Blostum si Lower Blow rembe Blosum a >more __clivengent specter cine present + plvine-But In PAM tower species Muwuben of pam 2 Blosum__maabix at incliecdes thot secronce ch poms mucus more divergent species is Chore K — Vs BLOS UM. ~ PAM BLOSUM, @ Rased on Mutational @Based en the haubtiple «model _otevotution.” | alignment of tra Blocks @® Aaigned to back the |@ Ralgnec| to tind) Prosein's Cotutienany. oxigin. Cmseriredl _. Semqeund.. @ pam is bad en 1@ crood do be ised do Sequencts of £57 simi. Lempark —_elistant - ~ tani Sequences.prodein sirdluty, madeix. | \\Pox £9 3A_ simple rato eal ay Scare of +4. and. nen-ide AS cminws ene). A_raoxe cemplicated matrix. a fights scove_transih'on then dv_-transyeruion. at er 8) Andino ded Sindlantty, mahax;/ Artinc Matix ane move complicated becat 20 Arsing aticl coclecl: doxditie genetic oe sindilanity niadix for AR centaina 1136)". 9i-is um > one ngfices eprexent pedein strurhuni wey “ | coordinate — "nailer OAR ron me shruchiw A} pekewt < ABistanke ‘mabox : blw hse sequent A Bitkain ce —_naatniws ane used in_phiplo {{.=parametnic_— distance natthods_ ies ate osutt ira wie applvedt 0_< phenttic.) datq uaing a= matax | wh, poin=unlee _“chisteintey... these -cistans _¢ axe then | ae] vecemclled —to_procluce Qtree. dhe. distance, I pactn'x can _teme Rem ot sansa ah atten} Seunctr. __jncludin measured distance metric. analysis, ¥ “nl —h s-morpho amudus painoise clistance estoy (ita H fomurta applied dn cliscrede Maoephe- ata logical chanacten Or _guntic ditane Sony, Ver” Sequence 4 mertiction Fragnunt ox _abtaruyner claby =| f h adchs n0n. rally f en. @_Netghbe @ veamp 2w @ Fitch Moxgalianh nuthod - + fi'stan. moder “on a metsune sequenits being an MSA 2, fistance nudsrceitchr. Chess elinen_ignoxed an ail oe Bistance —ratthods ~do alla eltseai bing eet th that . --rates Closely Scnt__nteriom __mode_ancl lovely —raproduct — #ae__sbunved seqyuench quent}, Set = each _seqienes pair tree cynics unclen Hn branch bngtta| ancth btw uthose Sequents..Tainiag Mathocl ol uta Siv wneti wing of _evetuhien acy AC Un eighted Pain Gretip ma etic tan) and w PGMA (w natthod with Arita nhc. Meron) o “rooted trees and +e, ye onc 1t__cssccnten 5: = Ua euxhich the elistances i phe ant * te exer branch ene g "sf _ 3. fitch Moro tiash _iucinod :~ the itch ——.tutthod uses og welghted _ east square’ tox. clustering ebasecl_ a =O ae Rte distance . Close ——sutlated sequences are el welgdt in ee TNE yee Censbuctien POM te coxxect fox a increased inacerrracy, sli muasurting bjctant! ee bie clistountly —suleted Secuenees , ;d lire to been Aiinctel clivergence WS_tetunten parts Hs nd hy a dash (=) jn the : Since these clashes Keprese ” Ene bx dtnin__sequrence. 4 o Indels +> Ue $ duo types of nautahen_ po Ee do singetiati ns Oh _-tdlels. IF we a (insertion hak ot sae _point ons _of the ———_ bitie) _was identical 4e_ its __priinuitive hen S thon a trace _ can _satpresent the ¢ Ways of divengence_ ditt de wbeuk = third dine _ se ubstituhion _, de) nention.& tmportanct_of Gap'=_4 Gap. maximal in &_sjngle string, ae coxxespends _¢ nent sizes. censidens position bia Se treadea ea thie | fasion pan att__possible— of a Penalty wun of 5 Pacey given. aligamunt, atomic ‘\nsentien Og. S$ _q Lsubshing. nurtatienal events can__tvecd< gaps _ of auignnants £ top SPA Single nuutitien tan create _a_ BE Be is exe) supelitien A shings OF Bose pte famman,. plication con mesult yn the. 1G Unequal cams over in _meinsis. can tad < 2 intention ox detetien of shiings cf bases. AG Frarslocation cf ENR hi coitimasemes, > © Retmyiznus insertion. = S! ohemaeiies so?ee, Typo—o Olowatant Penalties. qc Md Hinton ee Affine age ot = @-¢ Cepver nou @ Prfile_Based vaniable Gap Penalties 2D _ Ceustant Grap_Penattyi= ais is thae_siniplet type ee gop penalty ,= a #ixecl__neqative Score ts given + apes #0 every gap _meganclluss ot _ig_tey Ege ATTCCTHA gee Hes AT—CCTGA —_ mac >> Gap ite 5 Find Alignment scowe ? a fi Alf gneanat score 2 4-1 - aha sere tals. incon Pen tn Cemmpaned tothe constant J pares st ie geup penalty considers, — Hoe Length of 2ath asention se deletion a es fore 14 tne pens fox each | eS ied amen is. ® and the Rae Seat th, it ¢ pen cty would tang ts of Agap © 9 °tneah (gah P bes me pre cuct & ©40.; 5 dts ATAC ‘ 4 se ) “4h gon LATHC) a Gap P' aly = XY 16 Avs. Total ap penalty, BXL £.9> atombinatm of Livivon 2 dbo acy “ @ Affine Gap Penaty - “Yhe most widely, Used Gp penalty _dunctien js_tha affine —Gap—penclty —chith —_vembines the _Cemponents tn _botta Har constr! —tind __Linean gap. peneelty cueing tht. fom = A+(6¥L)._ i. : this —inbo duces au) derma Ais _k lathe Cr. pening: Penalty, 8 iste Gop extension _fencuity and —L js _the _tungth of tae gap- z oe ce mal asotta~foganitrur ereaty = @ vex “hap fonds: «Uaing’ © the whifine Gap Penalty L requires —the assigning “ of _4iteh fixecl penalty: values fox both opening. 4 extending dhe. gap. ‘this. _can—be duo xigid for use in a -ictogical CETL Seas a an os ®Profile Basecl_Vaniable Gap Peralty Baan onthe staticticnl = Sndel oi proniss—x0m_—_raliltiple sequence al i pririnie FST BLASTS Senn bree Ox xs y* : — ruibet ya wo Pruutesgenasi "ahha, Plcatien,{ f ee. odlam “bias refer to the phenomenon fon, ane wed mo te yynenynout codon clyring, drantod , ) Topics Preclictive method of Nucleotide secypesr | » Repetative 2NA @ Coden bias getecting @ selecting func a * Predithve nuthad oF Nucleotide eae 2 @ Repetitive ond Non —xepehitive ANAL \ 3 Cin genome js modo_.y oh dchencal —cutted ENA_undl ite centain 4 basic -buile ling (AT, 0,0. ‘ eee, Oxden _o¥__teducnces of these —inthuihon. inthe blocies bases dremihe | geno WAL « t = Eukanyctic ENA AB vumenous uthich have tne 4cluntical Secluencer of nibrogt “new base. “thus secyurenees__ ang repeated seven] ime __and — cluctened dogethen (Repetitive =: ONA_seclusnan oceun, in _o 3 form .- Highty, Repetotive SNA Ca ae *epetcitive BNA Non - Repetotive SNA. ENA __sequonts * Repetitive =A pout *tha _2NA__is nap ot sequences dred are pil ¢aan_in_q millien Copies, | Geneme- Approximathy Soy, in fun an genet: In_more WH ranges‘a @ tuighly Repetitive sequences these sequent present in , copies { genome > shart sequences 3_biffenurt Bensity trem the vert. °F chromosome ANA called scutellite SNA > tocaded in hetero drematic egion of Has rbaumenic _xeqien 2 ang _not trans cxibed > Mon, satellite ANA comists of tanclery short sequence of 8-8 bp- tho xepeats jdentical . > _Vanintion this type anise clue do different _in ( the number of Unit —ushich ane highly vant able. ed aus BNA_ane called Mra caiclhite ov VNTR< | : £tA_ Fingerprinting - eae a pels corvbro mune] + nak — é Telomere . : > Genome that tentain thee —_cliffenent claret oft a ox _veonneal Ing differant naanuren than mes __voita onlay singlt copy, _sequencth. ; >. 3nstead ot having, a_gingte Smooth eok* tures Hewe —clintincde (an be seen» euch repoeuating a diffewat] nk Auer __xepetitien clark:Repetitive _®NA | ° | Tonterspensed vepect ae nies persed repect 4 — v fs MELUKCOME | [mics oF : ae oe chromosomes i (we PUMP papaya LN | . £ —>-sS minicaiellity — Criacrosadettitcs > microsatellites U-gbp) Cto-tovbp} eesmabh } eee Ctenclam —t | ies] * Tamdem sepeads :— } i. aise ates 1 ENA Bee: O-_padtern of two ox mort = surcleotide Is _nepe andthe 4 ‘ Hens ane & adjacnt fo ectth oten, ed > form ___dliffenent density. band en clensity quad” (centnfugat en Crem Buth nia) ~SakUite)@ Tandem. repeat > Sadettite PNA hy i} sctnboncunic DNA aes *Telomenic DNA > Mitypsateluide hort Lancle Length. pelyinox phism f i a + An Gbps geunatly cudvienatin @ Minisatedlites s- > lo ={eo bp 20 -sodcinus > tuchromatin —~_ Enh finge Vpaints > Tanclornty, xepeade { b chicpensed Clustow . Also.ceulted viv Tondo Repeats. > Inter spouted repetitive BNA‘ 9+ accounts _e* &o- Ho?) ot mammatio SNA ane scaftened xdrdonty, throug dre genonac. daw = = © Unles cna_fop-=:Loun_baiat pals eng « + _Copiet ane sinatlant bur nok tclent ccal so eciche : : Inky poud vepetitive. quws on nok stably integra — ted jn atta _ generat dup move Fea place _te place 2 Hoy can sonutimner nus tpg ol genes nosable elements) Clauss T-Ancunsy more 3 Rehortex uns po son nee and pasie) : me Copy} dnaiseucth i? _RMAL and then back do SNA Lier = using mest jranseniplare.) 40 jndequats inte the ac a a s + gener .minal Repeat» ony stpec: also ane adive in_mice Snieispersed nuclear: Llemenhs Pronts —LDRF4 an Nuclean flenaents (s.NE) CAxthncb ater tha dude necognind by dag RE en preachinnt Intenspensed fs, ex = Alu up of 356 bp tena, = Aint [non -autemous \_<-soobp z © . > of fines & SINEs vainly —_knouz._04 Guile__SNA Role : in seme COR oti | a4 Jncoxporoted Into movel_ qos uaa 2 nu) Funcienaty.. Ses ! Yt dirmuptien cf thee Element —-has been imaplita- $ =ted__in seme __gensbie diseases cind cancess.. 2 — 2 Tampons Cela tes)_Cout and pastel use drank = =posass_to_ make O staggened —stidey cut: 2) Modsnately repetitive Sequences: + 9+ present in ado < 1045, geneme. + tt make, 0-801 oct chnomo yemal_snA_in tuk —yotu: ~ Se Tero + this tani the _nepecte, MW z Scluntical but ans gia e mags aie as degre _of _sulationship . vaswer Hk mumben oF the Fanaily, Cin geuthern “blots). Ripb aa Nen_~ repetahive NA+ Fgh seqluncs au alse callid Singhe Copy BNA sequeox Luniqure 3$b_ present iv ot copies in > 4dt gencially {0} _prvtely plasnadl Inet! ent _€apy _ 2 has ths ULCLESO Ccton kineh'ca fuk sequence and js ch anacteri zed Yalu. ©) Unteyusas Secuuences*- Gone _seduencts. cincl tne __aclyacent Sequenct xedpixed doy thelr expremien ood, centalned in dhe _uunteue — sequunce olue_ 2 With minor exeptions , the genonus OF 5 —prokany ote ang —temposed entirely of — single pel cep Sec uennce “= > tn Contrast, suth_secjumaces comshitute of dhe total genome —jin_serng_sta_u cies, mere than 50% ct - uman geno aud tor. + 8 IMelanogaste1_qenenat- 4. Abundant mrNh_- (4000 -10,,600. copiet_pex coll). Q. Scance mRNA< 10 copies Icell_, thanefore. dant —m RNAI sepresont Gund. ethos woieln | = S. paajor product of the concurred. a) type ce > Housekeeping quis Cromatitudive® genus stun gun un =EE /| H—{ [ @_(opon BIAS Detection: crenetic Code = | ( any | Coden’ he triplets of bases ont cabled cade ete Genttic ode is redundant | deqentiate: rere x the 20 amino acid is coded by 64 differnt codon! 413 (61 codons encoding for. cmino acids plus 2 _ Stop_Coclons) singe “araino acid is coclod by nus than ene codon. thi recluncdan 4 oredres Une nesistance of to nuttotiens: the third coden eters twobble bares) can often be interchanged — caithout affecting the Prindary seuonce of i protein product tuobble _ Hypotharis f / bende _fodes- hung ane _na uni vorsealtay Pprefevud ox univer Sally avoided codons me Que of 64 coden 59 (64 ~Stop_coden endl Av" ant infewting, for studying, codon ius,| faite. |. Cp, \ccApacee [Cet Aw ACC ACK ACG Ae aw Gee aA ALG F A ut A. 4 LODON BIAS-+- Excumjples:- = Biffesunws in_ths frequency Synonymous coclen,| fuucine (1) Coden nage | : ' z | MM: extorupns pe Eat P- putida | codon Hig [ede | Rat Lf DUA [. a UUG | eu \ fa coe ¥f | U : cuA [L J : CoG, Ys_vatie IS ¢he abundone ot that caden ulate | baat codons “for _teuicine « 2 t 1 Pmamiony- Be nococews Acidex. Buchner A 2x0 butkort “94 eto agrt ies phir ae dehatoyenant_~ clunana mi . Escherichia ts 7 Cote K12 ABR &£ AAG codes for hysine x(oden_Bias!~ * "tht genetic code is qenenotly dens Va anieng organism bub dtreagth of: ar vanies blu? oxganisna &_acsose Gener siti Jenowk +Mu choice fey) Ane. auth each ¥AR _coden_is Suprwase - L more than ene_coden can Specahy Sasas cnung_actd-. . @den_ Bias! Gre_eoden sll be wsed_move forthe artine aad Cor cluning tani ahen) over '_toden. E-g3 Valines—QvU-— Gue~ GUA Qug tr ab ¥ RAN ETO EL ‘toden. Glas deecten_pal aite Aelecting funche leh? Gent Genome def" hie al Gaenamrics > _Bescipline ypir viel oY es 1 | fomatitd ) 1 Cte nucs -p Mok (UL biology £ Bove rat Gononutes | 5 ‘ Shucwral generues ! Furchenal gencnus q ths (deals with Aer gal h Genence | Coleals eanth 4 Baa Function > Yat fulph__dhs ough pul ts } | analy ss of cll expresso genes is_culse klar freunscoypsrner cusrlyrs Funchenal 9 Chem. gene to. dundion): Cunorne Expression Pricer Vez : +O eh | ees At_KNA uxt : tern a 5 SUCH toh yp @ Mlcrvasoray 9 a Bim ith ni assur rn MENA in ‘q Sap le that corey Fiver gene ox probe PNA ¢e Gniaint ore Perel to 4 Weegee,sav Spechronich,, f g ap lcs Affinity pwusrcation AS @ RNA sequencing’ 9t has takin over micmrornoy ¢ | ke ‘ Dee, Pd ndlog in xewnt ages 4 tet hero, lent cary do study Pramcenphen 4 « gen nator. f dong by Mesut seqytenuing, j sae ser wW } erro) Ceeqfusnn million, of qenenw jn Aun tinu) . Ws knockeut strateg - LQ) AUR: (enn nitnfersne ) methods can’ be wed & AS teonnonty vlna or knock daion Gene expresi wn Lo Susing 20bp osKAIA . 5 Replat @ Transcxiphonee | — @ Canene Curaly £1 { a ee @ Coren fetllg y