How to make a prediction from a single sequence and what

www.compbio.dundee.ac.uk/jpred4

How to make a prediction from a single sequence and

what the output means



Contents 1.  Short Guide (two pages)

2.  Detailed step-by-step tutorial with results overview

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1. Short Guide (two pages)

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How to run JPred

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1.Pasteproteinsequence

2.Pushtosubmit…


Short Guide •  Submitting a single sequence for

prediction is very easy: • Cut-paste the query sequence into the “Input sequence” field on the main page • Push “Make Prediction” button

•  For more details on the format, process and results – see the more detailed tutorial below, as well as other tutorials and the Help/F.A.Q. JPred pages

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2. Detailed step-by-step tutorial

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Submission

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1.JpredhomepageURL

2.Cut-pastetheinputsequenceintothewindow.

Jpredrequiresinputaseitherasinglesequence,cutandpastedintothetextbox,oramulKplesequencealignmentuploadedasafile(seethefollowingpages).Itisimportantnottocutand

pasteamulKplesequencealignmentastheformaQngcangetmessedup.

WhenpasKnginasequence,donotaddanycommentordescripKonlines,

butspacesandcarriagereturnsareallowed.Youcanalsouploadsingle

sequencesasfiles.

TheuploadopKontakesprecedenceifbothinputshavebeenfilled.

PleaseciteJPredifyouuseitinyourwork.

3.Pushthe“MakePredicKon”buZon


Searching the PDB

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1.BydefaultJpredsearchesthePDBbeforedoingapredicKon.Ifyour

sequencehassequencesimilaritytoaproteinofknown3Dstructureyou

shouldreconsidertheuKlityofmakingapredicKon.

ThePDBisneversearchedwith

alignmentorbatchqueriessothisopKonisignoredforthoseinput

types.

2.EvenifaPDBsearchyieldedresultsyoucanforceJPredtoconKnueby

pushingthebuZon


Advanced options

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1.ClicktoshowadvancedopKons

2.Clicktoselectinputformat(defaultis“Raw/Fasta”whichissuitablefor

submissionofsinglesequences)

3.SelectthistoskipthePDBsearch(seethepreviouspage.)

4.Providingan(opKonal)e-mailaddressmeansyouwillbenoKfiedofthefateofyourjob.Asimplesummaryofthe

resultwillbeemailedtoyouwhenthepredicKoniscomplete.Pleasemakesureyoure-mailisvalidandcorrect

astheJpredserverwillnotcheckthevalidityofit.

5.Providea(opKonal)namewithwhichtoidenKfyyourpredicKon.Ifnonameisprovidedarandomlygeneratedone

willbeused.Querynamescanonlybemadeupofalphanumericand'_'characters.Invalidcharacterswillthrowupanerror.ThisopKonisprobablynotveryusefulifnotused

inconjuncKonwithane-mailaddress.


Tool-tips

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Whereveronthesiteyousee“(?)”–ifyouhover/clickonit–atool-Kphelpwillappear.

Whenthetextofthehelpislong–youmaysee

“show/hidemore…”clickingonthiswilltogglethedisplayofmoretext.

Thetool-Kpwilldisappearshortlyahermovingthe

cursoroffthetool-Kpfield.


Job URL, submission/progress

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1.URLoncejobhasstarted.Notetheformat:itisJPredmainURL,followedby/cgi-bin/chklog?NAME,

where‘NAME’–istheJPredgeneratedrandomnameforyourjob.

YoucanbookmarktheURLandcomebacktoitwithintwodays(theKmetheJPredserverstores

resultsforyou).Ifyoukeepthepageopen–itwillautomaKcally

reloadshowingthejobprogressandeventually–results.

2.JPredesKmateshowbusyisthecomputerclusterandinformsyouon

whereyourjobisinthelist.

3.Atanystageofsubmission/runningofthejob,ifyourealizethatamistakewasmadeandyouliketocancel(re-submit)a

job–youmaydeletethecurrentjob.


Job URL, submission/progress

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Jobisinprogress…


Summary email

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Ifyouprovidean(opKonal)emailaddress,youwillreceiveanemailwithashortresultssummaryandalinktoalltheresultsandfiles

produced.


Results summary page

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1.Clickingonthelinkinthesummaryemail,orusingtheURLfromthejobstatus/progress–seepreviouspages,orsimplykeepingthejobstatus/progresspageopen–willprovideyouwiththeresultssummarypage.

2.OneofthenewaddiKonsinJPred4–istheSVGimageofresultssummarygeneratedusingJalview(seejalview.org).

Let’sgothroughresultsJPredproducesonebyone.NOTE:thescreenshotsshownareonlypartsofthe

results.

3.Youmaydownloadall(but*.PS)resultsfilesusingthelinktothe*.TAR.GZarchiveforyourjob


Jalview generated SVG

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FormoredetailsonJalview,andJalviewtutorials,pleasevisit:hZp://www.jalview.org/

www.compbio.dundee.ac.uk/jpred4HTM

L R

esults d

etails

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1.Characters'E','H','B'and'-'representextended(E),helical(H)andother(-)typesofsecondarystructurerespecKvely.Inthe

solventaccessibilitypredicKonstheyrepresentburied(B)andexposed(-)for

eachofthe0%,5%and25%solventaccessibilitycut-offs.

…

www.com

pbio.dundee.ac.uk/jpred4


Results: simple summary

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Results summary in PDF

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Results directory

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Youcanfindallthefilesoverviewedinthistutorialandmoreintheresultsdirectory(linkedfromtheresults

summaryHTMLpageaswellasarchivedandavailablefordownloadin*.TAR.GZ)

TheREADMEfileexplainswhateachofthefilescontains.


README

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READMEfiledocumentsresultsfilesdescripKons.


Jalview Desktop Application

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1.Clickingon“ViewresultsinJalview”willtakeyoutoaseparatepage,whichrunstheJalview

JavaDesktop(youwillneedabrowserthatsupportsJava1.6,thisincludesmostmodern

browsers,andJavainstalledonyourcomputer)


Jalview Java Applet

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1.Similarly,clickingon“Viewresultsusingin-browserJalviewJavaapplet”willtakeyoutoa

separatepage,whichrunstheJalviewJavaApplet(youwillneedabrowserthatsupportsJava1.6,thisincludesmostmodernbrowsers,

andJavainstalledonyourcomputer)

2.AllowJavaapplettorunandpush“StartJalview”.


Jalview Java Applet

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FormoreinformaKonandtutorialsonJalviewpleasevisit

hZp://www.jalview.org/


JPred help • For help on JPred please

email: • [email protected]

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Documents

How to make a prediction from a single sequence and what