Your name: ____________________

Take-home exercise #7: genomes

Bioinformatics M.E.:800.707
J. Pevsner
Take-home exercise 7 !of 7"
Base# on $ecture 7 !%e#nes#a&' Januar& ()' *00+"
,ue at the start of c$ass %e#nes#a&' Januar& (8' *00+
This exercise -i$$ .e /ra#e# an# is -orth (00 of &our /ra#e for the entire course !-e
-i$$ take &our .est five /ra#es from the seven take-home exercises". The format is
un$imite# time' o1en .ook2 it shou$# take $ess than an hour. You ma& stu#& -ith
c$assmates or other stu#ents. But -hen &ou ans-er the fo$$o-in/ 3uestions' &ou M45T
-ork a$one.
Ever&one in the c$ass has .een assi/ne# a 1rotein. 6o the c$ass -e.site to fin# the
accession num.er for &ours. 7ecor# it here: _____________ 8ts name: ______________
Goals of this exercise
Become fami$iar -ith TaxP$ot at 9:B8
Become fami$iar -ith the 6enome Bro-ser at 9:B8
Become fami$iar -ith the 6enome Bro-ser at 4:5:
Become fami$iar -ith the 6enome Bro-ser at Ensem.$
To/ether' these are the three main /enome .ro-sers. 4se them to ex1$ore &our
/ene;1rotein.
[1] TaxPlot at NCBI
<a= >rom the home 1a/e of 9:B8' c$ick ?$$ ,ata.ases !on the to1 .ar" c$ick
6enome c$ick TaxP$ot !on the .ottom ri/ht". The #irect 47@ is:
htt1:;;---.nc.i.n$m.nih./ov;suti$s;taxik*.c/i
5e$ect C. elegans !a -orm" as the 3uer& /enome' an# se$ect Drosophila an# Homo
sapiens as the t-o s1ecies for com1arison. Your resu$t shou$# $ook $ike the screen ca1ture
on the to1 of 1a/e *.
<.= :$ick on the s1ot in#icate# -ith the arro-. %hat is its main nameA ____________
<c= %hat is its si/nificanceA
a" it is conserve# in -orm' fruit f$&' an# human
." it is conserve# .et-een f$& an# human .ut not -orm
c" it is conserve# .et-een f$& an# -orm .ut not human
#" it is conserve# .et-een -orm an# human .ut not f$&
(
<c=<7e1hrasin/ of 3uestion c= %hat is the meanin/ !or .io$o/ica$ si/nificance" of the
TaxP$ot resu$t for this 1articu$ar 1roteinA
a" it is conserve# in -orm' fruit f$&' an# human
." it is more hi/h$& conserve# .et-een f$& an# human than .et-een either of
those t-o 1roteins an# -orm
c" it is more hi/h$& conserve# .et-een f$& an# -orm than .et-een either of
those t-o 1roteins an# human
#" it is more hi/h$& conserve# .et-een -orm an# human than .et-een either of
those t-o 1roteins an# f$&
<#= %hat is the 1ercent i#entit& .et-een -orm an# f$&A _________
%hat is the 1ercent i#entit& .et-een -orm an# humanA _________
Bint: the ans-ers are sho-n .& c$ickin/ the $inks at .ottom $eft un#er CB$ast*5e3D
<e= ,o a ne- TaxP$ot search of micro.es. The $ink is at the to1 of the TaxP$ot 1a/e: one
can choose .et-een micro.ia$ an# eukar&otic /enomes. ?$ternative$&' /o to the 47@
htt1:;;---.nc.i.n$m.nih./ov;suti$s;taxik*.c/iAis.actE(.
5e$ect a reference /enome of E. coli F(* !a harm$ess form of E. coli". :hoose as the t-o
s1ecies for com1arison E. coli F(* an# E. coli G(H7:B7 !a strain that is #an/erous to
*
humans". :$ear$& i#entif& a 1rotein that is #ifferent .et-een the t-o strains2 c$ick on it'
then 1rovi#e a screen ca1ture. %hat is its nameA _____________
8s it $ike$& to .e 1resent in the F(* strain or the G(H7:B7 strainA _____________
<f= 7e1eat this usin/ E. coli G(H7:B7 as the reference /enome. %hat is the usefu$ness of
#oin/ this searchA
[] The Genome Bro!ser at NCBI
<a= >rom the home 1a/e of 9:B8' c$ick Ma1 Iie-er !on the ri/ht si#e.ar". Then c$ick
Homo sapiens:
<.= Enter the name of &our /ene. >or exam1$e' if &our /ene is ri.onuc$ease' fin# the
EntreJ 6ene officia$ /ene name 79?5E(. Enter it in the 3uer& .ox !at to1 $eft"' c$ick
>in# !at to1 ri/ht"' then see &our ans-er an# fo$$o- its $ink !arro-" as sho-n here:
)
<c= 5et the sca$e to sho- ( mi$$ion .ase 1airs !( M.". ,o this .& $eft c$ickin/ on the $eft-
most vertica$ track' as sho-n !ova$".
K
<#= %hat /ene is imme#iate$& u1stream of &oursA ________________
%hat /ene is imme#iate$& #o-nstream of &oursA ________________
<e= >o$$o- the $ink !see arro-" to the Ensem.$ 6ene 7e1ort.
["] The Genome Bro!ser at #nsem$l
<a= Bo- man& exons #oes &our /ene have' as sho-n in the Ensem.$ 6ene 7e1ortA
<.= :$ick the $ink !see arro-" to /o to the Ensem.$ :onti/Iie-
<c= 5e$ect the o1tion !$eft si#e.ar" Iie- a$on/si#eLMus muscu$us. 5creen ca1ture !1rint
out" the to1 $eve$ of the resu$t. Gn -hat chromosome is the mouse ortho$o/A _________
H
[%] The Genome Bro!ser at &C'C
<a= Iisit the htt1:;;/enome.ucsc.e#u.
:$ick 6enome Bro-ser !at to1 $eft".
8n the 3uer& .ox' enter the officia$ /ene name for &our /ene. ?n exam1$e is .e$o-2 note
that man& sam1$e 3ueries are 1rovi#e# at this 1a/e.
:$ick su.mit.
<.= :$ick the $ink corres1on#in/ to the a11ro1riate /ene !see arro-".
<c= ,is1$a& tracks sho-in/ the kno-n /enes' 7ef5e3 /enes' an# human m79?s as
sho-n .e$o-. Your tracks ma& var&' .ut #o not a## too man& tracks. 4se the refresh
.utton as nee#e#.
4n#er the Iariations an# 7e1eats section' set 5e/menta$ ,u1$ications to Cfu$$.D Moom out
as nee#e# to $ocate se/menta$ #u1$ications that occur on one si#e !or .oth si#es" of &our
/ene. 5creenshot;1rint the resu$t' hi/h$i/htin/ the re/ion!s" of se/menta$ #u1$ication.
<#= ,is1$a& exact$& (0 mi$$ion .ase 1airs of ,9? a11roximate$& !or exact$&" surroun#in/
&our /ene. Provi#e a screen ca1ture of the to1 1art of &our resu$t !resem.$in/ the screen
ca1ture 8 1rovi#e# Nust a.ove2 that one s1ans OK'0(0 .ase 1airs". Bint: use the
1osition;search .ox an# the Num1 .utton.
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