ebi web resources iii: web-based tools in europe (ebi...
TRANSCRIPT
![Page 1: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/1.jpg)
EBI web resources III: Web-based tools in Europe (EBI, ExPASy,
EMBOSS, DTU)
Yanbin Yin
1
![Page 2: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/2.jpg)
Homeworkassignment41. Downloadhttp://cys.bios.niu.edu/yyin/teach/PBB/purdue.cellwall.list.lignin.fa to
yourcomputer2. SelectaC3HproteinandaF5Hproteinfromtheabovefileandcalculatethe
sequence identitybetweenthemusingtheWaterserveratEBI.3. Performamultiple sequencealignmentusingMAFFTwithallFASTA
sequences inthefile4. Builtaphylogenywiththealignmentusingthe"AlaCarte"modeat
http://www.phylogeny.fr/5. Buildanotherphylogenystartingfromtheunalignedsequences usingthe
“one-click”modeathttp://www.phylogeny.fr/;ifyouencounteranyerrorreports,trytofigureoutwhyandhowtosolveit (hint:skiptheGblocks step).
Writeareport(inwordorppt)toincludealltheoperations,screenshotsandthefinalphylogeniesfromstep3and4.
Dueon10/11(sendbyemail)
2
Officehour:Tue,ThuandFri2-4pm,MO325AOremail:[email protected]
![Page 3: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/3.jpg)
Outline
• Handsonexercises!
3
![Page 4: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/4.jpg)
Pairwisealignment(includingdatabasesearch)tools
4
FasterSlower
LessmatchesMorematchesBLASTFASTASSEARCH
BLATBWABowtiePSI-BLAST
PSI-SearchHMMER3RPS-BLAST
![Page 5: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/5.jpg)
5
http://www.ebi.ac.uk/
Tothebottomofthepage
Clickbynames(A-Z)
![Page 6: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/6.jpg)
6
Thisisaverylong listoftoolsScrolldowntofindFASTA
OrCtrl+F andtypefasta
Wearegonna tryFASTAtool
ClickonFASTA[nucleotide]
![Page 7: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/7.jpg)
7
ClickGenomesWe’regonna searchArabidopsisgenome
![Page 8: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/8.jpg)
8
Clickonthislittlearrow ChooseArabidopsis
Gotohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faandcopythefirstseq (CesA)andpastehere
Changeheretoprotein
![Page 9: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/9.jpg)
9
Tfastx:allowframeshiftbetweencodons
Tfasty:alsoallowframeshiftwithincodons
Toleratesequenceerrors
Good forfinding pseudogenes
http://www.ebi.ac.uk/Tools/sss/fasta/help/index-genomes.html
![Page 10: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/10.jpg)
10
Should befinished veryquickly
Rawoutput (plain text)Graphicalpresentationoftheoutput
ShowEMBLformatofthesubject(hit)Showalignment
![Page 11: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/11.jpg)
11
Inthealignment, lookfor/ frameshift\ frameshift* stopcodon
Weareattherawoutputview
Inorder toalignthequeryprotein tothesubjectgenomicDNA,reading frameshavetomove1or2baseahead(1baseinsertionor2baseinsertion)
![Page 12: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/12.jpg)
12
BLASTgivesshorteralignmentbecauseitsalignmentbreakswhereitseesframeshifts
![Page 13: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/13.jpg)
13
GobacktothetoolA-Zpage:http://www.ebi.ac.uk/services/all
Ctrl+F andtypessearch
SSEARCHisacommand intheFASTApackageimplementing Smith-Watermanalgorithm
Ssearch canonlydoprotein-protein ornucleotide-nucleotide searchesSlowerbutmostaccurate
Canonlydopr-prornt-nt search
![Page 14: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/14.jpg)
14
GobacktothetoolA-Zpage:http://www.ebi.ac.uk/services/all
Ctrl+F andtypeemboss
EMBOSS:EuropeanMolecularBiologyOpenSoftwareSuiteEMBOSS:TheEuropeanMolecular BiologyOpenSoftwareSuite(2000)Rice,P.Longden,I.andBleasby,A.TrendsinGenetics16,(6)pp276--277
EMBOSScontainhundredsofcomputerprogramsforsequenceanalysis
![Page 15: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/15.jpg)
15
Needleman-wunsch algorithmSmith-Watermanalgorithm
Equivalenttothebl2seqcommandoftheBLASTpackage
Let’stryneedlefirst
![Page 16: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/16.jpg)
16
Globalvs localalignment:• inalocalalignment, youtrytomatchyourquerywithasubstring (aportion)
ofyoursubject(reference)• inaglobalalignmentyouperformanendtoendalignmentwiththesubject
![Page 17: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/17.jpg)
17
CslA:539aaCesA:1089aa
Gotohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faCopy&pasteCesACopy&pasteCslA
![Page 18: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/18.jpg)
18
- gap.Negativescore:positivescore|identical
ThisisdifferentfromwhatBLASTshowsthealignment
Notadatabasesearch,sonoE-valueisreported
Thisisneedleoutput
![Page 19: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/19.jpg)
19
Thisiswateroutput
Thebestwaytofind theoptimallyaligned regionsandcalculatethesimilaritybetweentwosequences
![Page 20: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/20.jpg)
20
Selectheretotryblast2seq
![Page 21: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/21.jpg)
21
Gotohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faCopy&pasteCesACopy&pasteCslA
Chooseblastp
![Page 22: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/22.jpg)
22
FragmentedalignmentsThisblast2seqoutput
![Page 23: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/23.jpg)
Multiplesequencealignmenttools
Foundationformanyotherfurtheranalyses:phylogeny,evolution,motif,
proteinfamilyetc.
23
![Page 24: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/24.jpg)
24
http://www.ebi.ac.uk/Tools/msa/TheMSApageshowsninetoolsandwe’regonna tryClustal Omega,MAFFTandMUSCLE
![Page 25: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/25.jpg)
25
![Page 26: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/26.jpg)
26
Youcanalwayscheckthehelppage
Gohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faandcopypasteallthe9protein seq here
Thensubmit
ThisisClustal Omegapage
![Page 27: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/27.jpg)
27
Thisiscalledclustal formatofMSA
ColorAAbasedonchemicalproperties,e.g.acidicAAinblue
Checktheevolutionaryrelatedness
Gettextformatsummaryoftheresults
![Page 28: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/28.jpg)
28
Txtformattodescriberelatednessandcanbevisualizedgraphicallyasatreegraph
Matrixtellshowsimilareachpairofseqs is
Bothcanbecopypastetonotepadandsaveasplaintextfile
![Page 29: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/29.jpg)
29
![Page 30: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/30.jpg)
30
ThisisMAFFTpageYoucanalwayscheckthehelppage
Gohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faandcopypasteallthe9protein seq here
ChangeheretoClustalW
![Page 31: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/31.jpg)
31
IDsweretruncated
ForcethefirstMresiduealigned
![Page 32: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/32.jpg)
32
ThisisMUSCLEpage
Gohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.faandcopypasteallthe9protein seq here
ChangeheretoClustalW
![Page 33: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/33.jpg)
33
![Page 34: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/34.jpg)
34
MolecularSystemsBiology7:539,2011
accuracy speedMAFFT>Clustal Omega>MUSCLE>>ClustalW
http://mafft.cbrc.jp/alignment/software/about.html
SowhichMSAtoolshould Iuse?
![Page 35: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/35.jpg)
35
http://www.ebi.ac.uk/Tools/msa/Visualizealignment
![Page 36: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/36.jpg)
36
Youcanalwayscheckthehelppage
Gohttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa.alnandcopypastetheMSAbuiltabove
ThisisMview page
MView reformatstheresultsofasequencedatabasesearch(BLAST,FASTA,etc)oramultiplealignment(MSF,PIR,CLUSTAL,etc)addingoptionalHTMLmark-uptocontrolcolouring andwebpagelayout.MView isnotamultiplealignmentprogram,norisitageneralpurposealignmenteditor
![Page 37: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/37.jpg)
37Consensuslettersexplainedathttp://bio-mview.sourceforge.net/manual/manual.html#ref-output-formats
![Page 38: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/38.jpg)
38
AnotherMSAvisualizationtool:ESPript http://espript.ibcp.fr/ESPript/ESPript/
Clickheretostart
![Page 39: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/39.jpg)
39
Copyhttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa.alnandpastetoatxtfileandsaveitonyourdesktop,andupload to
Afterthefileisuploaded
![Page 40: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/40.jpg)
40
Anewwindowpopped out,viewinPDF
![Page 41: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/41.jpg)
41
Wejusttriedtheverybasicfunction.ThiswebserverhasmanymoreusefulfunctionssuchasdisplayingsecondarystructuresalongwithMSA.Tolearnmore:http://espript.ibcp.fr/ESPript/ESPript/esp_tutorial.php
![Page 42: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/42.jpg)
42
ExPASy:ExpertProteinAnalysisSystematSIBCollectionofexternal/internaltools
![Page 43: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/43.jpg)
43
http://expasy.org/
Clickongenomics, thensequencealignment
Thiswebsitecollectandclassifyweblinkstohundreds ofbioinfo tools
![Page 44: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/44.jpg)
44
Thispageliststoolsforsequencealignment
We’regonna try
![Page 45: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/45.jpg)
45
http://weblogo.berkeley.edu/logo.cgi
Uploadthefilethatwedownloaded fromhttp://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa.aln
Toggle thistoallowlogoshown inmultiline
![Page 46: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/46.jpg)
46
Clicktoincrease
![Page 47: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/47.jpg)
47
Youcanalsocopypasteasegmentofthealignment toweblogoNoneedtousetheentirealignment
![Page 48: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/48.jpg)
48
Pastethecopiedsegmenthere
![Page 49: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/49.jpg)
49
WithMSAyoucanbuildaphylogeny todescribetherelatednessofseqs
Seqs
MSA
Phylogeny
Graph
Wearegonna trythiswebsite
![Page 50: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/50.jpg)
50
http://phylogeny.lirmm.fr/phylo_cgi/index.cgi
Threemodesofphylogenyreconstruction
Trytheoneclickmode
![Page 51: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/51.jpg)
51
Oneclickmodeusesthesetools
Givethisjobaname
http://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa
Gblocks isaprogramautomaticallyeditthealignment
![Page 52: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/52.jpg)
52
![Page 53: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/53.jpg)
53
EMBOSS:EuropeanMolecularBiologyOpenSoftwareSuite
EMBOSS:TheEuropeanMolecularBiologyOpenSoftwareSuite(2000)Rice,P.Longden,I.andBleasby,A.TrendsinGenetics16,(6)pp276--277
![Page 54: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/54.jpg)
54
http://emboss.sourceforge.net/
EMBOSScontainhundredsofcomputerprogramswritteninClanguageforsequenceanalysis
ThebestwaytouseistoinstallitonaLinuxcomputer
Herewe’regonna trysomepublicwebserversthathaveEMBOSSpackageinstalled
![Page 55: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/55.jpg)
55
Manyothersarenotaccessible,butthisoneis
![Page 56: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/56.jpg)
56
ThisiscalledEMBOSSexplorer,whichisawebinterfacetosupportrunning EMBOSSprograms throughweb
350+programsputintodifferentgroups
Wewilltryafewprograms inthispackage
![Page 57: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/57.jpg)
57
Themostbasicone:translateanucleotideseq toanaminoacidseq (relatedtofinding theopenreadingframes)
Find theprogramtranseq inthenucleictranslationgroup
![Page 58: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/58.jpg)
58
Copyandpastetheseq inhttp://cys.bios.niu.edu/yyin/teach/PBB/nt-example.faIt’sanassembledtranscriptfromESTdataofsomealgalspeciesWedonotknowifitindeedencodeaproteinandifyeswhereistheORFRemembermRNAcontainsuntranslated region(UTR)
Chooseallsixframes
![Page 59: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/59.jpg)
59
Thisislikelytherightframe
![Page 60: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/60.jpg)
60
Ifthisisacorrectresult?Youcantakethent seq todoblastatNCBI
Puttheseq IDherebecauseitisinGenBank already
Chooseswiss-prot becauseitissmallerandhighquality
![Page 61: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/61.jpg)
61
ClickformattingoptionsChooseplaintextviewClickreformat
![Page 62: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/62.jpg)
62
Thisisthealignmentofourquerywiththebesthit,theframeis+2,sameasthetranseq result
![Page 63: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/63.jpg)
63
![Page 64: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/64.jpg)
64
ThisisthelongestORF
![Page 65: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/65.jpg)
65
ATGCGCTA
TACGCGAT
TAGCGCATReverse
Complementhttp://cys.bios.niu.edu/yyin/teach/PBB/nt-example.fa
![Page 66: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/66.jpg)
66
![Page 67: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/67.jpg)
67
ATGCGCTA
TGCGCTRegion2-7
http://cys.bios.niu.edu/yyin/teach/PBB/nt-example.fa
Region57-400
![Page 68: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/68.jpg)
68
![Page 69: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/69.jpg)
69
CalculateGCcontent
ATGCGCTAGC%=50%
Changetoyestogetapic
![Page 70: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/70.jpg)
70
![Page 71: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/71.jpg)
71
ATGCGCTA
16possibledinuc64possible trinuc256possibletetranuc
Defaultisdinuc
![Page 72: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/72.jpg)
72
Equaloccurrence:1/16
Application: scangenometolookforregionswithabnormalcompositions
![Page 73: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/73.jpg)
73
http://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa,copypastethe1st seq
![Page 74: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/74.jpg)
74
![Page 75: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/75.jpg)
75
PopulartoolsdevelopedatTechnicalUniversityofDenmark
![Page 76: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/76.jpg)
76
Google:cbs dtu
![Page 77: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/77.jpg)
77
http://cys.bios.niu.edu/yyin/teach/PBB/nt-example.fa
![Page 78: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/78.jpg)
78
ThislistsalltheATGintheseq,eachwasscoredtoindicateitslikelihood tobeastartcodon
![Page 79: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/79.jpg)
79
![Page 80: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/80.jpg)
80
http://cys.bios.niu.edu/yyin/teach/PBB/cesa-pr.fa,copypastethe1st seq
![Page 81: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/81.jpg)
81
![Page 82: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/82.jpg)
82
![Page 83: EBI web resources III: Web-based tools in Europe (EBI ...cys.bios.niu.edu/yyin/teach/PBB/ebi-tools.pdf · EBI web resources III: Web-based tools in Europe (EBI, ExPASy, EMBOSS, DTU)](https://reader034.vdocuments.site/reader034/viewer/2022052300/5a77f4157f8b9a93088e3a4e/html5/thumbnails/83.jpg)
Nextclass:ClustalX andMEGA
83