1?0′?c?!¨í,XrLh*ü Andreas D.Baxevanis Genome Technology Branch National Human Genome Research Institude National Institutes of Health Bethesda.Maryland ü?R ? ′ `7èob ￥)??<?,Q,X~oè?à4?b^?,Xc? à?-1s6?,X<?,Qc?0 !¨í?+bE-o!¨íE? F?à?6?ó|#?<?,Q,Xs6?èá1uWà ?G?!¨íE??c?!¨ íèF? ?1 21(?G￡,XJW,X*ó(=:K?Nl?_9AèèM6í? úeL?,X!¨íc?è?à?-è 0JLd ?b<?,Q,X2?43 ￥*ó,XG2?è1?bèQ )ú?·<?,Q,XEˉê??àJá ?--b ¤?t<?,Qè5à-è0J?t?￡,X,ìG<?,Qè,?,?Eˉê _o `*ó(=/?cV)4§ üCK9?E? ??,XKY<Q' á às6?,ìG,X<?,Q?-è0J`?c?!¨í,XP?z±\  3è?à ?1 í<?,QBü,XHt4§XEˉ> NX#èJè(e#E-o±\  3íb4è?Y4è4§X,XG??U?? ' èúd?5x,ìG<?,QBüêè\Y??UZ?·!¨í,X!7.BX?? ￥)*üb?c?!¨í,X/?c ?t\Y#o,X-è0JNZ 3è4±??D?"?F? ?b #?Eˉ!¨í? progressive alignment? ,X Vé?#?Eˉ!¨í,X??qC*bS*ü5ù*ü0!¨í,X<?,QBüc?Kè.Br, ü,X*ó(=:T,Xê5ù è?.B Aè2?43 ￥*ó:T,X,ìfG6(?á à1k"?￠á à?M6?·?E-?K?Nlè'!¨í,X c??? CYE??tê? ?G?!¨í?èíbAu1k,X?ì?\??*ó+#? ürL?0è1k "?? üAu1kEóz `9?k?G!¨íKè?"G>5è  ?y ?C?ó,ìE￥,X!¨í?á1u?4?S*ü ,X??"?èS*ü5ùF??NOu??4§p,X!¨íè ′a ? ?.T0?o1?  ú??U ,Xè?Jí±\,X  3? +b:#G?b?"?5àá s)úèE-G? ?A|A???F?ú)??,X/?c??à￠?t?c?!¨í ,X?"???èy? ??2??,Xy*ü<?,QBü?￡?-1,X?'ê? ,X?"?è? aA|A?? tKYC4E?,X?"?è ′4±??D@?,X1k"?á6?E??((=,XDG￡? ü0′4§F?úú? ??èAo4?,X?c?!¨í,X1k"?? #?Eˉ!¨í?"? CLUSTAL W CLUSTAL W1k"??t?S"ˉS*ü,X?c?!¨í/?cè ü?)?U,XAu1kG ?TF? ?1!C S*ü?E-t/?c ?b#?Eˉ!¨í,X??èk?2??c?,XEg9èíb!￡?tc?Eˉ> ?G?!¨ íJèAu1k4§p? ?bE-o!¨EWèAu1kk?tC±/?-?L è ??Z!￡íc? Bioinformatics: A Practical Guide to the Analysis of genes and Proteins Edited by A.D. Baxevanis and B.E.E. Ouellette ISBN 0 471 191965. pages 172 188. Copyright ?1998 Wiley – Liss. Inc. NI-?è 1/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om ,XG2?èbè ?bF?E￥t9?"?èE-t-?L >*ü9Au1k??t2?43 ￥*óEY}??E-tEY} ?èt a ?1A?rU,ìE￥,Xc?è' a1 ?G?!¨íU,ìE￥,Xc???è4??!¨í¤o ? .è' aG??!¨í??tt9,X!¨íèq ?2O|?Vpt9,Xc?EW?èFw!?′+eK?è? NOt90N!1E?hc?,X??èt90N!?NOy ?0N!?5.ú `0N!=)5.ú? ü4± ??D???èS*ü5ùá? ü!¨íêt94§XμCè0N!?>9Sy*üZ ?1?)? ü . =??ê  l ′?0?,X(M!^!_ ?1 ?0N!5.ú#Q,X!_ ?è? <-1èE-o!_ ?è p ?/ E-t(M????4￡, ü,X0N!,X=) sí\1T )è ??U üFwoUY ?6? ü4§X6?? ,X!&?=)0N!èE-o0N!=)5.úAu1kY!5B?n,X? Z?4? ?b UNIXG ?,X CLUSTAL W,XS*üè5×<%??￠ ˉ/?á à(=/?9$d,X UIA<?,Q?? 2OèT?è Xenopus laevis `p=??E- ˉ/?Eg9c? ü?t )(à,X[êè0?A/? ?1 y ?,X?,X?/?è' a ü UNIX¤/0ú?;> clustalwè*ü ?NO;> Q?!?,???9° ) : ********************************************************************* **********CLUSTAL W(1.60) Multiple Sequence Alignments****************** ********************************************************************* 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: 1 EY?9° ),XEYNM 1(Sequence Input From Disc)1Eg9?U!¨í,Xc?èEY? a??)?c? Eg99° ) : Sequences should all be in 1 title. 6 formats accepted: NBRF PIR, EMBI, SwissProt, Peat son (Fasta), GDE, Clustal, GCG MSF. Enter the name of the sequence file: UIA.seqs 2?43?¤/*ü YA/? ?1y ?,X?è' a?¤K?Eg9c?,X[ê áè üE-G?c?Eg9[ NI-?è 2/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om ê á UIA.seqsè?oEg9E-t[ê áè#)T?/A? a[ê,XE?/?è' aE¨ 29° )è E-êè*ü ?1EY?EYNMEˉ> ?c?!¨í : **************** MULTIPLE ALIGNMENT MENU ***************** 1. DO COMPLETE MULTIPLE ALIGNMENT NOW (Slow / Accurate) 2. Produce guide tree file only 3. do alignment using old guide tree file 4. Toggle Slow Fast pairwise alignments = SLOW 5. Pairwise alignment parameters 6. Multiple alignment parameters 7. Reset gaps between alignments? = ON 8. Toggle screen display = ON 9. Output format ooptions S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: 1 ￠E-?&?,?è*ü ü;> ?c?!¨íêY\?EY?,X7?+è_9Aèè ü Multiple Alignment Parameters?è*ü ?1rL0N!? `=),X5.úè?? ü4??EY}?êú!; ?/?zA?a ?1C?E??tc?èEY??tú-?L ? BLOSUMê PAM?èJè ?1EY?'? t?"!_ ??)??ê5? ü?t(M?!&?êè ú?U;> (M??5.úèVpL??Uè?U5.? ?ú? ü Pairwise Alignment Parameters?è*ü ?1A×H*üb6!¨í `?!¨í,X5.ú `0k ·??? ′ üE-t_$è?à"uY ?1*ü9?/?à ?!¨í ?D,X?)μCè ′!8 ? YEY?EYNM? ”Do complete multiple alignment now”??EY?EYNM aè/?c? ü#) T/XêEY}?,XE?/?è' a??,ó!7,Xc?!¨í? CLUSTA W4§3êè?/?4?,X!¨í4§pèTE?,X_$,X4§p/ ü ò 8.1? ü!¨í??è ?o!&?>?A?ó ?ê ú&?èE-o?A?ú?/E-o!_ ? üc?4±íêP?z±,X?VpE¨ 2,X!¨í?)?t?,X0N!êá5×<%E-o<?,Q,X?)?-1μCè*ü  ?1a? !7 ?Dè' aE¨ 2/?cè,?W úE ??4?,X!¨í? CLUSTAL W (1.60) multipls sequence alignment hum U1A MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ mse U1A MATIATMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQ xla U1A MSIQEVRPNNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDELVSRNLKMRGQ NI-?è 3/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om dme U1A MEMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQ * * *************.****************** . . .***** hum U1A AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKR EKRKP mse U1A AFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKR EKRKP xla U1A AFVIFKETSSATNALRSMQGFPFYDKPMRIQYSKTDSDIIAKMKGTFVERDRKRQEKRKV dme U1A AFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKKVKPPKPA ******* **.****.***********.* *.*.****.**.***. ** .* . hum U1A KSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPP mse U1A KSQETPAAKKAVQGGAAAPVVGAVQ PVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPP xla U1A KVPEVQGVKNAMPGAALLPGVPGQMAAMQDMPGMTQAPRMMH MAGQAPYMHHJPGMPPP dme U1A PGTDEKKDKKKK P . * * hum U1A GLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPG mse U1A GLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILELTNLPEETNELMLSMLFNQFPG xla U1A GMAPGQMPPGGMPHGQLMPGQMAPMQPISENPPNHILFLTNLPEETNELMLSMLFNQFPG dme U1A SSAENSNP NAQTEQPPNQILFLTNLPEETNEMMLSMLFNQFPG * . * . .*.***.*************.*********** hum U1A FKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK mse U1A FKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK xla U1A FKEVRLVPGRHDIAFVEFDNEVQAGAARESLQGFKITQSNSMKISFAKK dme U1A FKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK ********.********* .*.*..**...******* ..***.**** ò 8.1?1 ˉ/? U1A c??2??,XEg9c?èS*ü CLUSTAL W?c?!¨í/?c ak,X!¨ í4§p?±\?UP?,X!_ ?!5B+ó ??A? üc???,X,ìh!5Bè±\?/á",X!_ ?+' &??A??9? MultiAlin NI-?è 4/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om MultAlin?"?3 ?b*ü?2?? ?G?!¨í??,X??' a ?b ?G?!¨í,X'úEˉ> ?tú  ?,X6.2O?'c?F?ú?2O aè??Eˉ> ?c?!¨íèAu1k??c?!¨í,X?tc?!¨ í,X?è ?bE-o?èG??X??é??E-tE?/?á?Eˉ> è,èúá üT è!8ê c?!¨í34§3Z? MultAlin ?1 ü INRA Toulouse,X?t)?)×5%&?T\?? ;> è?U!¨í,Xc?Y'; FASTA,X ?>2lC?tc?Eg9Yè' a￠?2????9° )è*ü nE?',X ?Dè!¨VEg ??è ?EY,XEg9?èé*ü,Xú-?L 1 ?0N!? `=)5.ú,Xú???D*ü ? ? BEg9c?,XE°E￥G2?èEY?á à,Xú-?L ?' aèc?>¤xáu <Tè'?c ?!¨íE¨ 2êè?Au1k?t?7èc?J/ ü!¨í,X???_9AèèV ò 8.1/,X*ü CLUSTAL W!¨í,X à ,Xc?>¤x4- MultAlináu <èy ?5,?,X!¨í ?DèJ4§pV ò 8.2/è ü?7èc?èYc?F? G!,X!_ ?,ìh,X!5B*ü!8!_ ?,X?m+!?></è?? DF? G!,X*ü?m+!?></è à è0ú ???? `ú?></±\ a·èK' ?V ò 8.2T?,X ò_? \aè*ü?/??"?ú?k,X!¨í4§pJá`<? ??U ? üb CLUSTAL W üp=c? ?Z?tKSzCYE? 10,X0N!è5à MultAlin ??Z?tKS0N!è5àèè MultAlin ?1k !¨ CLUSTAL W? 20t`<,ì à!_ ?,XfKóè'' èE-Já1E-?/??"?!¨ oê?/??"?ì C^èE-Y?UG?¤:,X?tá?,XA±Nlè G￠Eg9c?,X?Bü? ￥èh*üá à,X?"??k á à/?z,X?s?A:",X*ü ?EY?81Ft1K àêS*üèJèí?4?,X!¨í4§p01? !71óE??Gp? ?' ` ? !M6 -E?,X?"?íb?c?!¨íUY*üè*ü ?NOr)?eL?Q(à0?,XEg9c?è?U E?E??2??,X BLASTêJW,XDBge2?è?U ürP`xG?,èy0??n?èYt?,X? "? ?19? a?t )(à,Xc?èJè ?b!8c?,X?)?'ê ?èE¨ 2Y,X<?,QBü? ￡è`?¤t(M??"?n,X?G!¨í?\?êíèE-o?"?á/,XC±/?G2?JM2￠_ > ,X??,XDBge2?EO?9? a? üE-?F?úè?àA|A??/??"?èF?e2?(M!^DBg 19? ac?,X?' ` ?,Xè'' 3?/?￠??,Xc?μCEˉ> <?,QBü?￡ú2O,XY o,X?"?? ProfileScan ?b4￡L,X[êúd,X Gribskov?"? ,ProfileScanS*ü?/?/? pfscan,X?"??R?t<? ,QBüê GL,X1A?c? à?t[êg,X,ì? ′!8 üe2?L??UY?t[êg?1? t PROSITEè?t ExPASyDBgèE?E?S*ü?' `c? ??AìV?4??ú*ó(=:?G?? ,X!&? L?ú2O×1`t Pfam , L?Z<?,QBü4§X 3?￡èaJW L??"?Y\?á à,X è??,X<?,QBü4§X 3,X!¨í`<Y1`?,Xè5àáqM47?|ê,X?)ú?"?è!7 ′ E- è Pfam ?1Y 500?5!,?èE-o!,?,XBüG￡UQ? ?b PROSITE ` Pfam,Xe2? ?1E?E?A?K? ProfileScan,XNI`?èM ?L??U?51T ),XEg9 c??*ü[??èê5ù?t? ?è!¨V?t SWISS PROT ID?*ü ?1EY?e2?,X#ó zèEY?E¨ 2:+,X G!ê5ùY G!è*?7?ùàE?+ ,X???ZAèaEg?,X?è?à )? ü ? PROSITE2?43¤x?2O,X&á?A?D<?,Q,Xc?0? ?e2? : normalized taw from to Profile | description 355,9801 41556pos 6 612 PF00012 | HSP70 Heat shock hsp70 protein NI-?è 5/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om ,ó!7E¨ 2,X PROSITE5,?kJáàèEg?G? ?Yk"??,XúèE-t!ót1? raw? ,Xú,ó!7+e2?êS*ü,X'ú-?L Au1k?9,XèèμCê,XD+ “normalized”è G1è1E? 4-?Z*ü ü?t?-1??,XDBg ?1?R,X ?6?,X G!,XD,?è ? T9Aèè1C^?èJ' ￥*ó,X Q′)[C^??_9AèèVp1 355èJ' Q,X′ )[ ?Y 1.94O 10 349?D+ “from” ` “to” ?/?1A?c? ` G!,X[êG? ′,X! &?? BLOCKS BLOCKSDBgy*üZ +,XVéèí<?,QBü?￡Eˉ> HHnè5àá ?qC*b )t,Xc?D? +,X??9$dbètBF!,XVé &#0;?'? motif?è?'E? ??!?!ü ?GLc?,X±\,X  )è1Y?n,X<?,QBüs6?ê5ù4§X?'E-o9$db à??￡,X<?,QBü,X?'!¨íê ?áé90N!?èJ4§p +× +?!¨íè5àác?D?\aè?)?t(à0? ,X<?,QF? ?1ù ??tê5ùè?t,X +èíhbW,X!￡?ts6? `4§X?'? BLOCKSDBgD9$db PROSITE,X5,??'S*ü?tóHCw,Xc?Eˉ> BLOCKSe2?êè1A? c?? àDBgY,X + ü?) ?6?,X!&?Eˉ> !¨íèíb!￡?t!¨íF??S*ü!&?(M ?ú-?L ê5ù PSSMEˉ> 'ú? PSSM `E-:!M6 -E?,Xú-?L ?_V BLOSUM62?,XG?? ? übèJú5×<%Z ü4-n,X!&? ú1Y?t G!1 ??t4-n!ü ?GL 4B +,X !&?,X ?6???Y ?bE-/?6?,X?"?,X ???F???#!_ ? 4B!¨í<?,QBü +,X? t(M?!&?,X′)[èE- üF?ú,X4§? ?,X úa,Q? BLOCKSe2? ?1E?E?A?K??SL? ò,X Fred Hutchinson6?+?-è0J?,X BLOCKSNI`?èE-t5% &?\,èyèA?;> ?bc?ê5ùGKA?,X?2??Vp*ü üEg9êS*üZ DNAc?èa ? 1?aS*ü ?tF+??-?èe2? ?5Jò?á1u;> e2?,X?tc?E??tGKA?è?s ,Xe2?ú?E¨ 2,ìh,X +è ò 8.3/Z?t_$? üE-t5,???t Y%?2? ?'è/? 2O ?G[?J\?è′> YNNcú??A? IDè AC ` DEè4-?ZE-t +·><,X?￡,X4ymè BLOCKSDBg"?`-? `?￡,XAo4?￡E?× BL> 4-?ZGb4??E-t(M?,X +,X s?c??' ,XμC? ?D width ` seqs></ block,X?z?*ü!_ ?Au1k?è1 ?E-t +Y??c?D ,?èy?943Au:Y? `X?KSz,XμC×? ac??><è ?/?íhbE-t(M!^ ?',Xc?F?úè!￡?> ,X?F?E-tc?,X SWISS PROT"?`-?è1?t!_ ? üHtc? ,X!5Bè' ac?D1 ? ?b!&?,Xc?G?èE-tG?*ü 100zè 100></c?C± /?E-t5x'?E°×"??Yoc?> Y0N> ?F?ú!¨í>6.L? ü?CKè ü!￡t6.L?è 80% ,Xc?!_ ?,ì à,X? MoST MoS ?'e2?1K ê5ùm0 MoST)è?t UNIX/?cè*ü9Eˉ> DBge2?1?R±\,X?'? E-t?"?S*ü!¨íc? +?!¨í +è alignment block?è ?1?4???D,?1,Xc?è!￡? tKS/èYc?KSz?NO?7èè ü,?!E?á6?éEˉ0N!?E-t!¨í +*ü9{*ó?t<?,Q BüG?-?L è' aíYc?Eˉ> -?L ?￡è￠,??<?,QBüDBg??e2?èí!￡?tKS/,X (!?E?E?t `E? ü,XG?-?L 2?kJú?VpR ü43Au:T:+  G!bc? +,X c?èE-oc?3?>t9c? +?e2?`?t~)? aèG?-?L ?NOG??Au1kè' a G??Eˉ> e2?èE-tE?/? ?áEˉ> è,èa3Rá43Au:?:+,X G!c?!6èE-t E?/? ′5à üDBge2?E?/?á?/?3?,XμC? ü;> MoSTêY?t ?1A?5B,X ?D!¨_5è5></NXó,X<. G!D,?>NX#,X,ór G!D,?? ′ MoSTe2?NXóú? /?Aè ′á?aR?,Xc?è ?áE?/?ú?4? !6?è15,XEY? úG??U?Vp5tP?èe2??ê 5àá /è? a?éEˉ,?? DBg,XYc?èFS!<. G!,X?t?"?E?#?r?5è??3 G!,XDG￡ `BüG￡è Vp ?6??)?ê ×r?5? NI-?è 6/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om MoST Q?> 6? : most database block [method] [seg] [cutoff] [i#%] > outfile üE-G? database?a?Ue2? ??tDBg× block?a ?YEg9!¨í +,X[ê á *ü FASTA? ,| × ?EY,X method ?D?aZa Au1kqC*!5B,XG?-?L ?Vpát?aè5,?úEY ??)??t(M!^!_ ?,X ?6??,X Dirichletú×èEYNMé*ütG ? Gribskov?"??èEY NMé*ü BayesiantA?D?"?èEYNMé*üqC*DB,XtA?D? _è7?b;> V)EY?è ü MoST,X s? ?5×:YAo4?￡E?è?*ü hA1S*ü5,?è?14§p,XBüG￡è' a5×<% ú ? ?D× seg ?D?ae2? úh*ü segE?$?1k"?è seg?5,??></?G?è seg></ ?GG×Kü cutoff?aTM6￡E?,X!¨_5è|9$??EY? ü r0.1 r0.5×? aèS*ü i#% ? DúíEg9 +Eˉ> L$ è!¨VèVp?n i80%è ü4? ?Y,ì à!¨??b 80%!>é*üèE- tEYNM ?1 ü?)?￠?t(=/?9$d,X,ì àc?êèY 5BDB2?43,XA?? ò 8.4/Z?t MoSTEg?,X_$?Eg?[ê\?y  2hZ??,X Q?èA??G? MoSTè? ty?t E|??y?9,ó!7,X +è `F?Y?tNqê,Xc?è?A? 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ALSCRIPT üy !¨íê¤oZ\Q,X&I#??*ü ?1?n+'èF?ú !¨í,X?èEY?LEèrt[A??èrt0ú ? `> D1 ?Np8F,XEY??<Q' ALSCRIPT Dá6?{*óê5ù4êEe!¨íèW ?1Au1k??7èc?Jè*üE?',X??/ G!b?7èc ?,X!_ ??!7.BS*ü/?c ?1á/c?,X¤o(MUè!¨V+ 9Kú×ê5ùc?μ ?? ò 8.8/Z?t ALSCRIPT Q?[ê?,X_$è Q?[ê>ú?·?tFEeF?úè/?!9Px  `!9Px?!9Px? Step1? Q?{ Z!¨í,X'M6B`?+' _ ?è+'??èA?)n ?1 ?Np8Fn11è!9PxE?4-?ZEg9[ê? BLOCK_FILE, +[ê?,X!5B1 ?!¨íEg?,Xm 9[ê? OUT_FILE, Eg?[ê??!9Px 2 (Step2) a!¨í,X(MnF?úYGè!¨V ? à!￡? tc?,ìF?,X? ?è4-(Mn,X!_ ?ê5ù  3'T?êLEè4-!¨í?T"?G?1 ?Au1k?7è c??YE-o_$F?/ ü ò 8.8?"??Fwo"?G?> ?> !?A??èWà1T ) ?4? Z!￡?t·-? +,X0*üèE-o·-?F?+BE?,X??D Q?F?S*ü,XAá"?m,X?C3 ü BOX_REGION Q? aM6,X ˉtD+/c? ?o  3> àL?è üE-G?è1?t BOX_REGION Q ? aM6 6 3 15 8è??￠1Ytc?,X1At!_ ???1?tc?,X1 ht!_ ?' T??mQ,X[ê ?1,èy> ALSCRIPTS*üèE-o[ê ?1￠5%Tkè3 ?1+ ￥×,X UNIX(7?ú? ALSCRIPT ` MacBoxShadeS*ü,Xc?_$? ,Xè/?cBüTá? ,Xèy c?3 á? ,Xè ò 8.7 ` 8.9,X ?\a,X?a A? `>5 ú??? MacBoxShade!¨EW? ?S*üè ′Y ′2?F?íA±6?,XèEYNMYL$×5à ALSCRIPT¤oZè?,XEg?EY NMè!7V/,X Q?[êè:4a ?nEg?,X?L??U?n,XêKè0·??rL Tè ALSCRIPT Q?[ê ?1+??4??èE-o??S*üb?t!¨í o?t!¨íè ??U*ü íD+0??U,X? èE-?t\??,X{?4§p?a EY?!¨í?1KqC*b*ü ,X? 4?h*üL??U &#0;?UEˉ> E?Eó ##????#E??Uk1Y?(BüG￡,X ò6? 1?0′#] ?,XYGAòNl,Xf6(5%  ? !¨í?"? ? alignment method? HTTP5%  Clustal W http://www2.ebi.ac.uk/culstalw/ MSA http://www.ibc.wustle.edu/ibc/msa.html MultAlin http://www.toulouse.inra.fr/cgi bin/multalin.pl ?' ` ? (motifs and HTTP5%  NI-?è 9/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om ?5×[)? Bairoch.A. (1997). The PROSITE database: Its staus in 1997. Nucl.Acids.Res. 25. 217 221. Barton.G. (1993). ALSCRIPT. a tool to format multiple sequence alignment. Protein Eng. 6. 37 40. Corpet.F. (1988). Multiple sequence alignment with hierarchical clustering. Nucl.Acids.Res. 16. 10881 10890. Gribskov.M.., McLachlan.A.., and Eisenberg.D. (1987). Profile analysis: Detection patterns) BLOCKS http://blocks.fhcrc.org MoST http://ncbi.nlm.nih.gov/pub/koonin/most/ Pfam http://www.sanger.ac.uk/Software/Pfam PROSITE http://expasy.hcuge.ch/sprot/prosite.html PROBE ftp://ncbi.nlm.nih.gov/pub/neuwald/probel.0/ $è/?"? (presentation methods) HTTP5%  ALSCRIPT http://geoff.biop.ox.ac.uk/manuals/alscript/alscript.html BoxShade http://ulrec3.unil.ch/software/BOX_form.html MacBoxShade ftp://ulrec3.unil.ch/pub/boxshade/MacBoxshade E@6*ü (conversion utilities) HTTP5%  ReadSeq http://dot.imgen.bcm.tmc.edu:9331/seq util/Options/readseq.html NI-?è 10/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om of distantly related proteins. Proc.Natl.Acad.Sci. U.S.A. 84. 4355 4358. Gribskov.M.., Homyak.M.., Edenfield.J.., and Eisenberg.D. (1988). Profile scanning for three dimensional structural patterns in protein sequences. Comput.Appl.Biosci. 4. 61 66. Henikoff.J.G.., and Henikoff.S. (1996). BLOCKS database and its applications. Methods Enzymol. 266. 88 105. Higgins.D.G.., Thompson.J.D.., and Gibson.T.J. (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266. 383 402. Luthy. R.., Xenarios.I.., and Lawrence.C.E. (1997). Extracting protein alignment models from the sequence database. Nucl.Acids.Res. 25. 1665 1677. Sankoff.D. (1975). SIAM J.Appl.Math.78.35. Tatusov.R.., Altschul.S.., and Koonin.E. (1994). Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc.Natl.Acad.Sci. U.S.A. 91. 12091 12095. V T? NI ?? NI E¨ 2,? ) E¨ 29 X NI-?è 11/111?0′?c?!¨í,XrLh*ü 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1?0′?c?!¨í,XrLh*ü .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om