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Abhi Journal
Abhi Journal
BLAST-EXER C ISE ·
J. Poi::i 1 your brow:,er to t he X C · · - -"o. I
PQA(:T\CA<-- 6 · I) ( BLAST scn·cr. 11 ,. , ·
· .
2. Jn 1he B :i.s rc lll:ts 1 scc ii on, click th . .· · · - Al\•1 ncb1.nlm.:D.!I'•_Q O'J{~~~T .
3 . .Enter accession num be r( ) e protein BL.-\ST (b la~1p) fin k.
E3LRST: nBLAST I f6lflS-T
A-\ W To s-tt..ld'f
h
BLRST-toir sEOtr i~
- -~
. -
8'XPS ~ ol.o.--fo~ c.~~ •
------ .
s , or FA....CTA sequence(s) in :t Qu e Se
You h3·,·e two ways to pas 1e., ~
~ s ~quencc to ihc bla~1p Serve r·
• Jf ::,our sequence rs airc:idy in a d:Jtab:isc ·o u e;i . . .
bl aslp. For ou r ex.,m 1 ·)
.
.
ry quc ncc "me.Jo".
4. Choose Swiss-Pro! fro111 pull <l ow n menu (from Cho ose Search Seti
enobles- a. '">E'SeCCYchrE-Y -to c-omp::ne o ~~ ~E=t,(f= LJ...JtH, °' 5. Selec t bl:l s tp from Program Selection (Algorithm)
11 1pz::,Y'f cn- eta.ta~ of- se q,u EY>C<?s, arc:i rctf'rl-t-{fy \t'o-rony
6. Click BLAST button
SBt)JerT~ -+'>"1C& ')-c'~b1e .....+--v-i.e qµ.ery ~ n<R q_k:,Q\JE' o..
Sequences s imi l:!r to th..: query that b!as ip r<.:turn s ar..: the hits or 111u tch ,•~ - -rn..: d:n,,b:!s .: ) ou
cea-tain -+h'J-€5'hDlol .
search is the targt.!I dtd//b u .)C.
7. Go to print prc\·ic \1· ;.?n u pri:ii page u o. :i~ per tir e i11 s !r u1.: 1i on of c:\:!mi:l(:r.
TI PES OF BL AST
1· Nucta:>+<de &.AST (blos+u)
- OTHE R £ X,-\J,1PLES for BLAST - in sulin , h :i cmog lubin e tc.
2 · P'YOtein 8LAST(lo los+p)
3. r:bs-i-HGn - ~ c i-Pi'C. lcerwve 8LAST (BP5I - BLAST) - __,
~ CTtiO DO LOG.-'/
A· OA 1A Ac ~s H- lon
AS ,.
I· Ge -tO NC B\ he me po.9e one ). Clr'c-f;=_ Cf'\ ~L
2. - En-\-e'Y acc ~ss -lcn 0u -
m ~ af-. 'fC} jy ~€ r'l ce o-P-- i ~ .i{")
- -
-------
J8
PRAC'11C'A-L- '1-
M SA E\T l{C!Sr:-1
'T 'A?n sect,u- ~ . Enter o m; acccss ion number (or scq11cnc1.: 11::i m..:) pa line. f·or our c:-- ::impk, '-'·'-' 1.: ntcrcJ
P20-172 . PS00 79, 1'02626. P026 I 9. P4 3305. PJ2930, Q91 -182 , P02620. P329J0.
11-tEORi - \n b,otnfo"()fY)0.~3 o se~ ence a!t'~nrner"rl- ls o ~ ---·
:t. Click Retrieve
oF olTO.ngin~
~ rro:ry ~ffi<.'E'3 of- ON Ft, RNA- OY pnrtei~-
- - - r'dfn+if-y :::e31onS' of- s\("y')\.lcxY\+-j ~ rno..-.r be con~9U~cE' of- 5. Download FASTA :rnd save the fik (011 desk top)
+urc+rono.J , s+>,u.c+u-c-E> ar-. evotlttfana ~ ~ohbn.sN p s bek.uE'en _ 6. Point your browse r to the EB! Clnsr:i! W scn·cr p:i~c :it ,,w,,.cbi .:ic.us,shi.:J...b.. 7 1..:
-----
--¼e ~ ~ . s . A1 t9~cA ~ '2(')«::;; of- r,uct.e::>-Ho(-e a,, arYr.ir-0 a.o8 Clust:! IW p::igc appears.
're•sfdu f'~ 0."2€ -+-t p t'ca.11_)' -re~ e ~ ~~c...u~ c....or+01n a r n ~·'><'. 6. C li ck Drowse :111d upl o:id the file from the dtsiin:ition whe re you h:i, ~ ~:1, cd lht
Cja.p.s a~ cnS'E'rlEt,! ~ -tt.e. -..eslol<-A.Q.S' so -+{.raj- <)€S'(d ues FASTA format file
I
3 ~ oJfhy se_~E n< -e cu r9n ~( )t- 5.
oJ qo nW ,rn -to pnx:lu<'e lri1'9W 1
o ~ (:'.Y)<:e o.1 )9'r) me n+ cv~~ aJ ''-f
~I
coMfu+a:Haro .1 Of '~O C: h<? S' --t
·,,,-t o ,..+- u)C ) o:::.t4;€q_~E ? S' .
aJ_!_90i'Y"l~rns, <J-)h,c h ~ -+c a1 9n
i' G io ~ 01 1 9 0 ~ - _G1o_~
'e , o- .e l'Y )() ~ u ~ efu -( LL) her-. --+1
0e.
BJ t?6 , ~9 td Ll2 ·,
0 e. Vf?6'-( S€w -,< f't'X --
---- -
u9 W '( a-f - ~ a ) '3 t-z.E>.
~~
1
n ~ <J,1-'-'2~ _'?e-k ,~ _s,~ Ho.-Y o, rd ¥'O
_ac ~v e
).. f"< '€c ira t'\i~ C..
+r ee s .
- - -
i - S1" E-P3 \~ \LC, L\/ {?D ---- - -- -
-- --- -
~ \)AT A BC0 U\S\-r \ON :
I. \ '1 N'S A- ~ 6'w ~(2 a,l 1'9 nrr,Qi) t-- ~ rrcre --\--lra n -+u.Jo ~~ ~00
~ dore ~ a +{mQ .
2- R.et')(\'eve arcl SO.'-le ~ ol~t~ ed ~..1.1-\-i'pl.e. ~ €¥)~-tt"~
Uni Prot- Li..R\os r-t-e ir-. f-A.ITA- +erYfY\oJr ·
3 · C.ot"( o 1Jd f?:~ ~
Cl1'ck. ori FASTPr O.<'ld
Qrr::E'S In
-- - - - - - - - - -
- - ----- ---
--- - ----
21
~e ~ e ~- ---- - -- -----
pR\N~\ Plc - \-\- rum~ ---tD <::~o~·s'n on e'-C\u+-?a flO!', ~ C<\'3" J o --rc:,-o
,,.
'=\~t'~) ruF Q\-(' CJ(\~ , i rd ivk)( w aJs ~ r~ ~ a.mi"{ S( ~ ci- ~ ry-,:. ---:
~CXB:)U f2E-
p. . QA-TR ACC\)O\ST\ ON ·.
1• _Mor:J ~ oJ,·i f'\~ IY)e-+hW ~uC'"~ a.~ c tus+cu O n ~ , i ~
ence
___used-to consrouct- o.. ph:Jl?:--f: ~c. -ttee °f'O~ ttGO'l s ~~L, ~
- -~iT::_'~ ___·____ ____ __
_ 2.... __ Re-h-e,ue ~ 31!.e~ s~~ i n ~ ~S.TA -f'o6,-Y-Xxt .of._.\;re ~~
_Q-f---k--Q ~"9oniSr- ns of- wh1Ch-t1 rl2_ Ph't\OC\e"r \etiC. cv)Cl.l'i -s tS. -h-ee. l""')~
-+o 6e --fcuro(. Turs rs 0e+')(<eved. -P-ro('(\ uri i P>ot- E-6\ \r\0,--:n.2 ~9..~ .
-- - - -
ES\ ~,u~\ O rnQ:f='-- ~
~- Co?-1 ord po.~ ~ e above seqµ~ce tf"'\
---- _O r d ~ ~ NS'A ·
♦
v,o.ve o. rornrron a n ~ bu:r rr0j ho..'-fe °'-""-lsen_ h··~~n: Ae-,Hj 't7-j_ ,,,,
Put! co,•, '1 the display me/'lu and c-'iange the rende1ing to "ribbons"
\· '3-\-ac:M- SPD~\f
You shoulo t;,e abie to see that} cu l1a, ~ betn-shee t, alµha- hellx, and a short
frag~e~, o' ON.\ 2· cy.J -t-o_?OB oru ~eve I HF\" J.
5 Pu!I oown tile co lors menu and cllange the coloring to "structure". The PDS \1-fe) (oo-+c., - load IHft.-l • pc.A'o(rnenu..fi(-e>c,?e<'I
co'crs ne o show that TSP ,s composed of a-helices and b-s hee ls.
Si->uc-ft.ue Ond, 3e!E'C't- I KEW . pd b)
~· (\ \'Cl::: Clrl -the ¾Ee Ct.('YSOY C -
6 C ick en :ne Rasmol Command V\lindow and typ e. (type th e bold tex t and oM-rol b..ct-to~ O""--f-he -tco\\co.Se Ord
press en:er ~ /l'Ylove/erito9e l½s::.i2....,rre -pl<:+v~.
- :ype- restrict protein (:hrs command cu ts away all atoms except protein 4\ Ope,--l-he C'Qif"Jtn,\ funel (l...(,J/rdo..v f'V\eru')
atoms\
5'·1O pe(') -+Ire A-\(91"'\~J wirdow IYl~) -
S ;; ;>=- select ONA (selects DNA)
---~-
6· saect- cu I
-
r)..J
-,
C \l'ct:1
__
n9 0(\ -+vie l,...,c_
I - C::.' ....lf"'>
~ - ' ><..A'C. G
f- --
O · O- lo'ce.lS i~-+1,,,e
Fu I dc1·.n :.re display menu and set the display to ball and stick. Note that
m s char;;es ,ne rendering only of the selected atoms (in t11is case, the DNA).
~ nttrol f'anel 1~ 9o-ki ~ u '$€.1.e(j- _ > ~1 •
_ _ _1_·,_S_elect- cr'Yi b'oof\' -flror() ~ Cbr)+rnl ~n'2l C
m o::. o l".--01 \u" OI"\ -++<z ~
;Q :ype- color blue chan~es the color oi the selected atoms lo blue. Try green,
·e □ cyar e:c - ' ranQ.( -\-o.b) d
~1 ,ype- select hetero selects non-DNA non-protein atoms _ 8· C'f?lm€ __9(~~m-ca~()')11 (c.PIC, ~ ~C':t<J.&€ ,o.ct~,b\~)
i2 Pull do,·. n ,re display re,"'u and se t the display to "spacefil l". Now you can ard oli'.spa
1 a~~J:.S\--c.J....u CA +m.ce a<'ll.'1 ,.,1,.-ou.;_~~,- ---')(e,~
see the oxygen a:oms irorn 'Naier molecules. In an x-ray diffraction · 7
~rcl<?a- CO\O-.A'Y ar-d. Disp..a
1 ~ s ~--t<',€,l'i; ·
1
e9erimen: h:,c'roge:1 ai0rns are generally not ob servable, so they are lef1 out _ o_,€
of the coordma:e '",le 9 J Click - s19() d- r3\.-,cu.J 1 arid <'std.<?' in co~~'_e._o.0e\ ( S't'Y btA·u....,111
13. type- co lor red changes the water oxygen colo r to red ld1's~ 'Y)
1.1! Lei's take a look at the DNA in the absence of everything else. ~ 8::'t- (t&-- r v , ~ ~~ os-+v'\e 'oU:ttDm o f - ~ cc~\ F<n<?I)
15. rype - res tricl D NA ..µ.,,e NAQ- lnniwttfY 1'-IA&-201 -2..0~
16. Pull down the display menu and sei the display lo " ball an d stick". 11 • Click o.9a.in~ rshCL.u 1 <s id'c'"\ ox)~ \aide C'Qi\Gl..V"""
PRePA-l<--A7lON OF P \C..-k.Fl.
· 6u~Nf'9 --\-H?rn _·
___16· Wre n -----tt,,,e 8?\C< 2S ore{ co---:d ', ~ deYe .\O f'
--+t---ez,-e ~~~
oil CAdd CVO fE'd chill / O{rp_ ~f \r")C:-h o+- ~ ~~ rvux 't-\ -~~kk/;,,
-I
soi+~ f~lr ~~ .
13·_orx:e -++e c'n,\\\c>s a-ise- ~ ~ ' , sof+ ord, ter-rcf) j u.>.'02 ( 'n().tt- ~(\')
ock:! ~ i ~ e ~ . --
- - ------------------
-+o_o.."ot i
- - __: ~rl- srras h.5 - + - c ~ ard. k~~ wh:l\e rnix+< J~ S-hi~
_ . __
wYtli "-\ of- .snu_CQ
~ SN"JCSh<~ ~d ~ 0- h~ us slu ~~ of- a.A\ t:91Cb\,E'm-3.
Of'P''-1'7) p->eSS U€ (J.)V1Ch hQfS in sepa ~r::9 SOLl@ -fro<ll +he crl-v\-<?Y
- -- - - - - - - - - - - - - - - - - - - - - - - - - - - -
C O LCL>U'l7 PD -
. ·. ~ =-X
beo.keo 1 s+-roin<?r . _ ----- 10 0
. indr'c-cd-O r, O · t N N0-CH-{ . I
c- Chen-i,coJ s - ph<::na'pH->al0 n - -- :x. = 3.75
on-+<ne f>0-9.e. t -e A- _ _ _ _ __ -=- O· I >c f3."Y x100 xo·6 Y (O sC06bi c o.cid C'oY"is+o 0+-)
~ lnhierrr ~
L
3. fO ~O<, of. T-S'·S ~ nd o.a'a.H)_ t:,.J ~ ..frcivn O'r€
?,2. 31
Gt,tovo ju...,., l -
c·
cl,. !'loe ones) , t . . u ~ ' C:
C: 0.C'fd, ~~.
/-.'>'
; o... n ~ ! l " k
In ....w-,e v-,-e3e rx:e of- 0 1'"'1 o.c1d 0 0 o'- 3-J..°iC('y J p,2C+i (') - rr O ~
0 srnc::lll m,n1 ~ , T"(UJ nE>-c--.
~ \ o.\cohol , ve:s;?}. spoo ' 1
i. · (:;,;u.O..'-I CA ('2...SO C)IYIS.') ~ Cl-lloed (tAJ i4--h S'>=-tr,')
2 · Cover: c...ul+-v, u..lo±e o ·
PROCEDURE- 3 · P-ctd ' / ~ --t-e p c.\-h'\ aclo( .
i . Cube -+ire. --m.~,
"- .u.... a,-u
1 it::OCh'
- - J·~ enou9h u..X:d:€r --to C:Q\R~--+vi€.~lt- - l.-\ · B C\~ -t-n °' 'oOII CJ.rd ~t'Y\IY'ler -fcy l o <Y'll f) .
2 · Pdd 1/4 --to p Clt<iC acid -Ri°" 2..SG cyms- <=jUO.\.O.. C'rt->1C Ocld. ~r>S-to f; · '\"e'6"'t06YY"> o.J. C'O hd -\e"?t-'....+o VE'!"~ ?ro--{ f"'\ e .x;:+YCAcHOri
r:; . 2... ll..LJY\.f' ...foir<Y\Ed, so pecH n CO"<t"E'& ls. cY\~ Um
e~ ~ n oL..rl-- of----tn.J..ifs, espedol1 '1 ---fr'Grn --+hCR.s: -h-u.tt:s wh\~~
1 . -'· ~5 C\'C'r\ o{-- .s~Qv o.d.d 8:J / 10~9 rw :; o+- -ftui-+- p...tl P .
~ 1€ ~ In o.cid. ~~ l'2._ o.n acldic. pH !S. ~~ --fc~r~~,.., '6 ·.·. 2...11 'lm s4a_v odctru ('2...L<.9:9ms cl- 'ca\l~ ~u.i+- e -x--1-~c+
e~c-Ho'2.__wh8'1 ~'J joC'Yl .
9· Boilard "~'1
'V
u., µ+,, y:>\G.:l-€ ~ -f-
3 . Wren --++-e mt)\"\-{.(re comes-to o. loOil, pt.t+- i+-cn S'Gr-ne -Feiir- o.b:lLGt -1
\O rn in s . c oo\ - > stdo-e ir. s+eYt \\sB::,1. k:0\--{-{,€>
- - -------
PECT\N
Luviich T? duaJIJ ~ DS i-t- coo, . Tu ts '1€ -k. uO ~ { s a. 9e1 CA(" )d. -fe r
rn d rub te 'oaf-Ches ,