Introduc)ontoBioinforma)cs

ShifraBen-Dor

Bioinforma)csUnitLifeSciencesCoreFacili)es

LectureOutline:

•  TechnicalCourseItems

•  Sequences

•  Databases

– Thisweekandnextweek

Thetechnicalstuff

Thecourseismadeupofonelectureandanop)onalexercisesessioneachweek.

Theexercisesessionsarenotmandatory,theyaretheretohelp.Demonstra)onsoftheprogramswillbedoneinboththelecturesandtheexercisesessions.Theexercisesessionsareanopportunityforyoutodotheassignmentwithsomebodytheretoaskforhelpifyougetstuck.

Thetechnicalstuff

Ifyouareplanningoncomingtotheexercisesessions,pleasesendmeanemail:

shifra.ben-dor@weizmann.ac.il

TheTechnicalStuff

Thecoursewebsiteiswhereyoucanfindthesyllabus,lecturenotes,assignments,linkstothevariousprogramstaughtandtorelevantliterature.Itisalsowhereweputannouncementsandupdates.hOp://dors.weizmann.ac.il/course/introbioinfo/

•  ThiscourseisbuiltforBiologists

•  Backgroundwillbegivenonvarioustopicsasneeded,butbasicknowledgeofB.Sc.levelbiologyistakenforgranted

•  Ifyouneedhelpwiththebiology,contactme

Thetechnicalstuff

Requirementsforagrade

•  Youarerequiredtodoalloftheassignmentsandafinalproject

•  Thecoursegradeiscomputedasfollows:60%finalproject,40%assignments

Assignments

•  Youhavetwoweekstohandineachassignment

•  AssignmentsaretobehandedinattheWolfsonlecturehall,bytheendofthelecture(11:00)

•  Ifforanyreasonyouneed/wantanextension,talktomeBEFOREtheassignmentisdue

•  Anassignmenthandedinlateornotatallwillgeta0

Assignments

•  Youmayconsultwithafriendwhiledoingtheassignment,howeverallworkmustbehandedinindividually.Ifwefindcopyingthegradewillbedividedamongthenumberofstudentshandinginthesameanswersheet

•  Assignmentsshouldbeprintedandhandedin.Electronicsubmission(e-mail)willNOTbeaccepted.

FinalProject

•  ThefinalprojectwillbegiveninthebeginningofJuly.

•  ItwillbedueonAugust9.

•  Lateprojectswillnotbeaccepted

•  ThereisNOpossibilitytocorrectprojects

•  Ifevidenceisfoundofsharedwork,therewillbenocoursegrade

Announcements,Updates…

•  Anynewswillbeannouncedinthelecturesandupdatedonthewebsite

• Whatissaidinthelecturehallisthefinalword,unlessspecifiedotherwise

Ifyouhaveques)ons,comments,sugges)onsorcomplaints-pleasecontactus-theearlierthebeOer!

CourseStaff

MainLecturer:ShifraBen-DorMetargelot:

IritOrr BareketDassa

Howtocontactus:

Shifra:shifra.ben-dor@weizmann.ac.il

Telephone:2470or(08)934-2470Wedon’tbite!

Whatisbioinforma)cs?

Whatwillwecoverinthiscourse?

Whatwon’twecoverinthiscourse?

•  Detailedstructuralanalysisofproteins•  AlgorithmDevelopment

•  Highthroughputmethods

•  In-depthphylogene)csorevolu)onarybiology•  In-depthsystemsbiology

•  siRNA,miRNA

•  PromoterAnalysis

Skep)cismandcomputers

ThebiologicalthinkinghastobedonebyYOU

LectureOutline:

•  TechnicalCourseItems

•  Sequences

•  Databases

– Thisweekandnextweek

What“unitsofinforma)on”dowedealwithinbioinforma)cs?

• DNA

• RNA

• Protein

• Sequence

• Structure

• Evolu)on

• Pathways

•  Interac)ons

• Muta)ons

Examplesofbiologicaldatausedinbioinforma)cs

v DNA (Genome)

v RNA (Transciptome)

v Protein (Proteome)

DNA  RawDNASequence

•  CodingorNotcoding?

•  Parseintogenes?

•  Otherimportant

genomicelements?

•  4bases:AGCT

 atggcaaOaaaaOggtatcaatggOOggtcgtatcggccgtatcgtaOccgtgcagcacaacaccgtgatgacaOgaagOgtaggtaOaacgacOaatcgacgOgaatacatggcOatatgOgaaatatgaOcaactcacggtcgOtcgacggcactgOgaagtgaaagatggtaacOagtggOaatggtaaaactatccgtgtaactgcagaacgtgatcca

DNA/RNAsequences

•  Genesareencodedingenomicsequences.

•  Genesaretranscribedintopre-mRNAs(includingcoding,intronic,5’and3’untranslatedregions).

• mRNAsarespliced(intronsremoved)andtranslatedintoproteins.

• mRNAsarecopiedtocDNAs(inthelab)

TSS TTS

ATG Stop PolyAsitePromoter 1 2 3 4

ATG Stop PolyAsite

1 2 3 4

GenomicDNA

Pre-mRNA

mRNA

ModifiedfromZhangMQNatRevGenet.2002Sep;3(9):698-709.

ATG Stop

1 2 3 4Cap PolyA

5’UTR 3’UTRCDS

SourcesofmRNAs

•  Experimental– Clonenewgene– “Clone”genefromdatabase– RNA-Seq

•  Database– “Typical”cDNA– FulllengthcDNA– EST(ExpressedSequenceTag)– Shortreadsequences

mRNA

FulllengthcDNA

TypicalcDNA

5’mG AAAA

TTTT

TTTT

tag

AAAAtag

tag

SourcesofmRNAs

•  Experimental– Clonenewgene– “Clone”genefromdatabase– RNA-Seq

•  Database– “Typical”cDNA– FulllengthcDNA– EST(ExpressedSequenceTag)– Shortreadsequences

RNA

RNA,cDNA,andESTs

mRNA

cDNA

exon1 exon2 exon3

EST

EST

cDNAclone

GenBankESTs(ExpressedSequenceTags):~8,700,000humanESTs~4,850,000mouseESTs

AdaptedwithpermissionfromAdamSar)el

UsesofESTs

- predic)onofcodingregions- detec)onofalterna)vesplicing- clusteringtoform“genes”Problemswithclustering:- incompletecoveragebreaksgenesup- genefamilies

ProblemswithESTs

- lowcopynumbergenes

- rare)ssues- mistakes

- enrichmentof3’endsofgenes

- incompletecoverageofgenes

NextGenera)onSequencing

•  Generallyshortreads(thoughnowlongertechnologiesarebecomingavailable)

•  Sequencelengthsrangefrom20-25bpto75-100to150bpreads

•  Canbe3’endonly•  Canbepairedorsingleread

MatePair

Con)gsor“Transcripts”

FragmentRead

Pairedendreads

ESTvsRead

•  ESTshavelongercon)nuoussequence,sobeOertoseegenestructure(alterna)ve

splicing)

•  Shortreadsgenerallyhavehigheraccuracy

•  Bothcannotgiveapictureofawholegene

Protein

•  20leOeralphabet  ACDEFGHIKLMNPQRSTVWY  ButnotBJOUXZ

•  Stringsof~300aainanaverageprotein

  (e.g.bacteria)

•  Proteinaredividedintodomains

LNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSILNSIVAVCQNMGIGKDGNLPWPPLRNEYKYFQRMTSTSHVEGKQNAVIMGKKTWFSIISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESITAFLWAQDRNGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESF

Protein

v ProteomeofanOrganismv 2Dgelsv MassSpecv 2DStructurev 3DStructurev 4DStructure(interac)ons)

LectureOutline:

•  TechnicalCourseItems

•  Sequences

•  Databases

Databases:Outline

•  Introduc)on– DataandDatabasetypes– Databasecomponents

•  DataFormats•  Sampledatabases•  Howtotextsearchdatabases

What“unitsofinforma)on”dowedealwithinbioinforma)cs?

•  DNA•  RNA•  Protein

•  Sequence•  Structure•  Evolu)on

•  Pathways•  Interac)ons•  Muta)ons

AAGTGCCACTGCATAAATGACCATGAGTGGGCACCGGTAAGGGAGGGTGATGCTATCTGGTCTGAAGNucleotidesequence

Genes

mRNA

Proteinprimarysequence

Protein 3Dstructure

ProteinFunction

Acts as a tumor suppressor inmany tumor types. induces growtharrest or apoptosis depending on thephysiological circumstances or celltype, but both activities areinvolved in tumor suppression.

Involved in the transport ofchloride ions. Defects in CFTRare the cause of cystic fibrosis.It is the most common genetic diseasein the caucasian population, with aprevalence of about 1 in 2000 livebirths. cf, an autosomal recessivedisorder, is a common generalizeddisorder of exocrine gland function

SNPs

Whatdowewantfromdatabases?

Allofthesehavedatabasesandtoolsthatwerecreatedtoworkwiththem

Informa)onretrievalfromsequencedatabases

  Biologicaldatabasescontainenormousamountsofdata.

•  Databasesneedtobewellannotated.•  Databasesneedtobeeasilysearched.•  Datafoundindatabasesshouldbeeasilyretrieved.

•  Dataindatabasesshouldbeinstandardformats.

IntegratedInforma)onRetrieval

• Manydatabasescontainlogicalrela)onsbetweenspecificentries.

•  Oneinterface-connec)ngmanybiologicaldatabases.

•  Forexample:adatabasethatconnectsbetweenproteinsequence,proteindomain,proteinstructureandreferencedatabases.(Interpro)

•  Anotherexample:Connec)onbetweenreferences,proteinsequence,DNAsequence,andstructuredatabases.(Entrez)

000003 breast cancer 1, early onset000002 breast cancer 1, early onset

000001 tumor protein p53

Chromosomal location: 17p13.1

DNA sequence:

mRNA sequence:

Protein function:

brain -liver -lung -

Protein sequence:

Interacts with genes:

Protein structure:

000365, 025783, 004674

PDB 1OLG, 1OLH, 1SAE

Fields

External links

Internal links

A Database

AccessionNumber

Entries

Slide provided by Dr. Vered Caspi

CoreDataandAnnota)on

Databasesgenerallyhave(atleast)twotypesofdata:

Coredata:Thedatathedatabasewasgeneratedtoorganize

Annota)on:Extrainforma)onthatroundsoutourpictureofthecoredataForexampleinagenomedatabase,thesequenceisthecoredata,andtheloca)onofgenesistheannota)on

DatabaseIssues

•  Printedjournalsvs.databases

•  Directsubmissiontodatabases(e.g.GenBank,PDB)

•  Archivalvs.curateddatabases

•  Databasesthatpublishexperimentalresultsoflargegenomiccenters.

•  Publicvs.privatedatabases.

ForExample:ClassificaSonofGenomicDatabases

Databasescope

InformaSonsource

InformaSontype

ManygenomesOneGenomeOneSubjectOneGene

Directsubmissionfromscien)ficcommunityScien)ficliteratureGenomecenter’sexperimentalresultsOtherdatabases

MappingSequence&annota)onProteinstructure&func)onVaria)onsCompara)vegenomicsgenenetworks

Slide provided by Dr. Vered Caspi

UserInterface

•  Databasesearch– freetext– field-specific– sequence-based

•  Databaseoutput– text– graphics– dynamic

DataFormats

Therearemanydataformatsusedforsequences(bothnucleicandaminoacid)

•  FastaFormat•  GenBankFormat•  FastqFormat

•  (EMBLFormat)

FastaFormat

•  Simplestformat

•  Leastinforma)on

•  Startswitha>andsequencenameononeline

•  Thesequenceinplaintextfollows

>OB2T2GTGACAACATGTACAGCTGTGAGCGGTGTAAGAAGCTGCGGAACGGAGTGAAGTACTGCAAAGTCCTGCGGTTGCCCGAGATCCTGTGCATTCACCTAAAGCGCTTTCGGCACGAGGTGATGTACTCATTCAAGATCAACAGCCACGTCTCCTTGCCCTCGAGGGGCTCGACCTGCGCCCCTTCCTTGCCAAGGAGTGCACATCCCAGATCACCACCTACGACCTCCTCTCGGTCATCTGCCACCACGGCACGGCAGGCA

>TNRC_HUMAN P36941 (tumor necrosis factor c receptor)MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYYEPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPCDPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAELKDEVGKGNNHCVPCKAGHFQNTSSPSARCQPHTRCENQGLVEAAPGTAQSDTTCKNPLEPLPPEMSGTMLMLAVLLPLAFFLLLATVFSCIWKSHPSLCRKLGSLLKRRPQGEGPNPVAGSWEPPKAHPYFPDLVQPLLPISGDVSPVSTGLPAAPVLEAGVPQQQSPLDLTREPQLEPGEQSQVAHGTNGIHVTGGSMTITGNIYIYNGPVLGGPPGPGDLPATPEPPYPIPEEGDPGPPGLSTPHQEDGKAWHLAETEHCGATPSNRGPRNQFITHD>TNRC_MOUSE P50284 lymphotoxin-beta receptor precursorMRLPRASSPCGLAWGPLLLGLSGLLVASQPQLVPPYRIENQTCWDQDKEYYEPMHDVCCSRCPPGEFVFAVCSRSQDTVCKTCPHNSYNEHWNHLSTCQLCRPCDIVLGFEEVAPCTSDRKAECRCQPGMSCVYLDNECVHCEEERLVLCQPGTEAEVTDEIMDTDVNCVPCKPGHFQNTSSPRARCQPHTRCEIQGLVEAAPGTSYSDTICKNPPEPGAMLLLAILLSLVLFLLFTTVLACAWMRHPSLCRKLGTLLKRHPEGEESPPCPAPRADPHFPDLAEPLLPMSGDLSPSPAGPPTAPSLEEVVLQQQSPLVQARELEAEPGEHGQVAHGANGIHVTGGSVTVTGNIYIYNGPVLGGTRGPGDPPAPPEPPYPTPEEGAPGPSELSTPYQEDGKAWHLAETETLGCQDL>TNR1_RAT P22934 tumor necrosis factor receptor 1 precursor (p60)MGLPIVPGLLLSLVLLALLMGIHPSGVTGLVPSLGDREKRDNLCPQGKYAHPKNNSICCTKCHKGTYLVSDCPSPGQETVCEVCDKGTFTASQNHVRQCLSCKTCRKEMFQVEISPCKADMDTVCGCKKNQFQRYLSETHFQCVDCSPCFNGTVTIPCKEKQNTVCNCHAGFFLSGNECTPCSHCKKNQECMKLCLPPVANVTNPQDSGTAVLLPLVIFLGLCLLFFICISLLCRYPQWRPRVYSIICRDSAPVKEVEGEGIVTKPLTPASIPAFSPNPGFNPTLGFSTTPRFSHPVSSTPISPVFGPSNWHNFVPPVREVVPTQGADPLLYGSLNPVPIPAPVRKWEDVVAAQPQRLDTADPAMLYAVVDGVPPTRWKEFMRLLGLSEHEIERLELQNGRCLREAHYSMLEAWRRRTPRHEATLDVVGRVLCDMNLRGCLENIRETLESPAHSSTTHLPR

KnownIssueswithFastaFormat

•  Differentprogramstreattheheaderlinedifferently:

– Someread10characters,some30

– Somereadun)lthefirstspace

• Makesureyouhaveuniquenames!!!

•  Headerlinesshouldbeunder80characters•  Lengthofsequencelinecandiffer

@SRR2976060.1 1 length=202NAAGCTCTCACCCATGGAGACCAAGGCGATTAGGGTTTTTCTCTTCGCTCTCCTCCT+SRR2976060.1 1 length=202#1=DDFFFHHHHHJJJEIJJJJJIJJJJFHGJIIJ9DHIIIJJJJGIIJJJGIIIJJ

FastqFormat

Fourlines:1–startswith@andisauniqueiden)fier2–theactualsequence3–startswitha+andcanhaveaniden)fieragain4–thequalityofthebases

GenbankFormat

• Dividedintothreeparts:– Informa)onlines– Featuretable– Sequence

EMBL sequence formatRN [2] RA Wirsel S.G.R., Leibinger W., Mendgen K.W.; RT "Genetic diversity of fungi associated with common reed (Phragmites RT australis)"; RL Unpublished. XX FH Key Location/Qualifiers FH FT source 1..581 FT /db_xref="taxon:112223" FT /organism="ascomycota sp. 4/97-9" FT /isolate="4/97-9"