Motif search GENOME 559: Introduction to Statistical and Computational Genomics Prof. William Stafford Noble

One-minute responses Another class practicing loops would be good. x3 Pace was good today. x2 Now that we are learning loops I can see how we can start writing more powerful programs. I like the examples, they are getting more challenging. I liked the background mathematical explanations in the first part of the lecture. I also like the example using BLAST, made it easier to understand. Well explained syntax. Is it possible to break loops that are not most recent. The compiled list of commands is helpful. Maybe distribute such a list every couple of weeks. Getting challenging but still good pace. I just need to go practice these by myself. Practice problems good today. Loops are very confusing. Really good guidance and practice.

Outline Motifs – definition and motivation Motif databases Scanning with a PSSM

What is a motif? Set of similar substrings, within a family of diverged sequences. Motif long DNA or protein sequence

Protein motifs Protein binding site Phosphorylation site HAHU V.LSPADKTN..VKAAWGKVG.AHAGE..........YGAEAL.ERMFLSF..PTTKTYFPH.FDLS.HGSA HAOR M.LTDAEKKE..VTALWGKAA.GHGEE..........YGAEAL.ERLFQAF..PTTKTYFSH.FDLS.HGSA HADK V.LSAADKTN..VKGVFSKIG.GHAEE..........YGAETL.ERMFIAY..PQTKTYFPH.FDLS.HGSA HBHU VHLTPEEKSA..VTALWGKVN.VDEVG...........G.EAL.GRLLVVY..PWTQRFFES.FGDL.STPD HBOR VHLSGGEKSA..VTNLWGKVN.INELG...........G.EAL.GRLLVVY..PWTQRFFEA.FGDL.SSAG HBDK VHWTAEEKQL..ITGLWGKVNvAD.CG...........A.EAL.ARLLIVY..PWTQRFFAS.FGNL.SSPT MYHU G.LSDGEWQL..VLNVWGKVE.ADIPG..........HGQEVL.IRLFKGH..PETLEKFDK.FKHL.KSED MYOR G.LSDGEWQL..VLKVWGKVE.GDLPG..........HGQEVL.IRLFKTH..PETLEKFDK.FKGL.KTED IGLOB M.KFFAVLALCiVGAIASPLT.ADEASlvqsswkavsHNEVEIlAAVFAAY..PDIQNKFSQaFKDLASIKD GPUGNI A.LTEKQEAL..LKQSWEVLK.QNIPA..........HS.LRL.FALIIEA.APESKYVFSF.LKDSNEIPE GPYL GVLTDVQVAL..VKSSFEEFN.ANIPK...........N.THR.FFTLVLEiAPGAKDLFSF.LKGSSEVPQ GGZLB M.L.DQQTIN..IIKATVPVLkEHGVT...........ITTTF.YKNLFAK.HPEVRPLFDM.GRQ..ESLE   Protein binding site Phosphorylation site Structural motif

Transcription factor binding site motifs Transcription factor binding sites

Why identify motifs? In proteins In DNA Identify functionally important regions of a protein family Find similarities to known proteins In DNA Discover how genes are regulated Discover how splicing is regulated

xxxxxxxxxxx.xxxxxxxxx.xxxxx..........xxxxxx.xxxxxxx.xxxxxxxxxx.xxxxxxxxx HAHU V.LSPADKTN..VKAAWGKVG.AHAGE..........YGAEAL.ERMFLSF..PTTKTYFPH.FDLS.HGSA HAOR M.LTDAEKKE..VTALWGKAA.GHGEE..........YGAEAL.ERLFQAF..PTTKTYFSH.FDLS.HGSA HADK V.LSAADKTN..VKGVFSKIG.GHAEE..........YGAETL.ERMFIAY..PQTKTYFPH.FDLS.HGSA HBHU VHLTPEEKSA..VTALWGKVN.VDEVG...........G.EAL.GRLLVVY..PWTQRFFES.FGDL.STPD HBOR VHLSGGEKSA..VTNLWGKVN.INELG...........G.EAL.GRLLVVY..PWTQRFFEA.FGDL.SSAG HBDK VHWTAEEKQL..ITGLWGKVNvAD.CG...........A.EAL.ARLLIVY..PWTQRFFAS.FGNL.SSPT MYHU G.LSDGEWQL..VLNVWGKVE.ADIPG..........HGQEVL.IRLFKGH..PETLEKFDK.FKHL.KSED MYOR G.LSDGEWQL..VLKVWGKVE.GDLPG..........HGQEVL.IRLFKTH..PETLEKFDK.FKGL.KTED IGLOB M.KFFAVLALCiVGAIASPLT.ADEASlvqsswkavsHNEVEIlAAVFAAY.PDIQNKFSQFaGKDLASIKD GPUGNI A.LTEKQEAL..LKQSWEVLK.QNIPA..........HS.LRL.FALIIEA.APESKYVFSF.LKDSNEIPE GPYL GVLTDVQVAL..VKSSFEEFN.ANIPK...........N.THR.FFTLVLEiAPGAKDLFSF.LKGSSEVPQ GGZLB M.L.DQQTIN..IIKATVPVLkEHGVT...........ITTTF.YKNLFAK.HPEVRPLFDM.GRQ..ESLE   xxxxx.xxxxxxxxxxxxx..xxxxxxxxxxxxxxx..xxxxxxx.xxxxxxx...xxxxxxxxxxxxxxxx HAHU QVKGH.GKKVADA.LTN......AVA.HVDDMPNA...LSALS.D.LHAHKL....RVDPVNF.KLLSHCLL HAOR QIKAH.GKKVADA.L.S......TAAGHFDDMDSA...LSALS.D.LHAHKL....RVDPVNF.KLLAHCIL HADK QIKAH.GKKVAAA.LVE......AVN.HVDDIAGA...LSKLS.D.LHAQKL....RVDPVNF.KFLGHCFL HBHU AVMGNpKVKAHGK.KVLGA..FSDGLAHLDNLKGT...FATLS.E.LHCDKL....HVDPENF.RL.LGNVL HBOR AVMGNpKVKAHGA.KVLTS..FGDALKNLDDLKGT...FAKLS.E.LHCDKL....HVDPENFNRL..GNVL HBDK AILGNpMVRAHGK.KVLTS..FGDAVKNLDNIKNT...FAQLS.E.LHCDKL....HVDPENF.RL.LGDIL MYHU EMKASeDLKKHGA.TVL......TALGGILKKKGHH..EAEIKPL.AQSHATK...HKIPVKYLEFISECII MYOR EMKASaDLKKHGG.TVL......TALGNILKKKGQH..EAELKPL.AQSHATK...HKISIKFLEYISEAII IGLOB T.GA...FATHATRIVSFLseVIALSGNTSNAAAV...NSLVSKL.GDDHKA....R.GVSAA.QF..GEFR GPUGNI NNPK...LKAHAAVIFKTI...CESATELRQKGHAVwdNNTLKRL.GSIHLK....N.KITDP.HF.EVMKG GPYL NNPD...LQAHAG.KVFKL..TYEAAIQLEVNGAVAs.DATLKSL.GSVHVS....K.GVVDA.HF.PVVKE GGZLB Q......PKALAM.TVL......AAAQNIENLPAIL..PAVKKIAvKHCQAGVaaaH.YPIVGQEL.LGAIK xxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..x HAHU VT.LAA.H..LPAEFTPA..VHASLDKFLASV.STVLTS..KY..R HAOR VV.LAR.H..CPGEFTPS..AHAAMDKFLSKV.ATVLTS..KY..R HADK VV.VAI.H..HPAALTPE..VHASLDKFMCAV.GAVLTA..KY..R HBHU VCVLAH.H..FGKEFTPP..VQAAYQKVVAGV.ANALAH..KY..H HBOR IVVLAR.H..FSKDFSPE..VQAAWQKLVSGV.AHALGH..KY..H HBDK IIVLAA.H..FTKDFTPE..CQAAWQKLVRVV.AHALAR..KY..H MYHU QV.LQSKHPgDFGADAQGA.MNKALELFRKDM.ASNYKELGFQ..G MYOR HV.LQSKHSaDFGADAQAA.MGKALELFRNDM.AAKYKEFGFQ..G IGLOB TA.LVA.Y..LQANVSWGDnVAAAWNKA.LDN.TFAIVV..PR..L GPUGNI ALLGTIKEA.IKENWSDE..MGQAWTEAYNQLVATIKAE..MK..E GPYL AILKTIKEV.VGDKWSEE..LNTAWTIAYDELAIIIKKE..MKdaA GGZLB EVLGDAAT..DDILDAWGK.AYGVIADVFIQVEADLYAQ..AV..E Globin motifs

Splice site motif in logo format weblogo.berkeley.edu

Position-specific scoring matrix This PSSM assigns the sequence NMFWAFGH a score of 0 + -2 + -3 + -2 + -1 + 6 + 6 + 8 = 12. A -1 -2 R 5 1 -3 N 6 D C Q E 2 G H 8 I -4 L K M F P S T W Y 3 V

Representing a motif as a PSSM Convert these nine 6-letter sequences into a PSSM. Add a small pseudocount. Convert to frequencies. Divide by the background probability. Take the log (base 2). AAGTGT TAATGT AATTGT AATTGA ATCTGT TGTTGT AAATGA TTTTGT A 6 6 2 0 0 2 C 0 0 1 0 0 0 G 0 1 1 0 9 0 T 3 2 5 9 0 7

Representing motifs as PSSMs AAGTGT TAATGT AATTGT AATTGA ATCTGT TGTTGT AAATGA TTTTGT A 6 6 2 0 0 2 C 0 0 1 0 0 0 G 0 1 1 0 9 0 T 3 2 5 9 0 7 A 6.25 6.25 2.25 0.25 0.25 2.25 C 0.25 0.25 1.25 0.25 0.25 0.25 G 0.25 1.25 1.25 0.25 9.25 0.25 T 3.25 2.25 5.25 9.25 0.25 7.25 Add a pseudocount. Convert to frequencies. Divide by background Take the logarithm. A 0.625 0.625 0.225 0.025 0.025 0.225 C 0.025 0.025 0.125 0.025 0.025 0.025 G 0.025 0.125 0.125 0.025 0.925 0.025 T 0.325 0.225 0.525 0.925 0.025 0.725 A 2.500 2.500 0.900 0.100 0.100 0.900 C 0.100 0.100 0.500 0.100 0.100 0.100 G 0.100 0.500 0.500 0.100 3.700 0.100 T 1.300 0.900 2.100 3.700 0.100 2.900 A 1.32 1.32 -0.15 -3.32 -3.32 -0.15 C -3.32 -3.32 -1.00 -3.32 -3.32 -3.32 G -3.32 -1.00 -1.00 -3.32 1.89 -3.32 T 0.38 -0.15 1.07 1.89 -3.32 1.54

Scanning for motif occurrences Given: a long DNA sequence, and TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAG a DNA motif represented as a PSSM Find: occurrences of the motif in the sequence A 1.32 1.32 -0.15 -3.32 -3.32 -0.15 C -3.32 -3.32 -1.00 -3.32 -3.32 -3.32 G -3.32 -1.00 -1.00 -3.32 1.89 -3.32 T 0.38 -0.15 1.07 1.89 -3.32 1.54

Scanning for motif occurrences 0.38 + 1.32 – 0.15 + 1.89 + 1.89 + 1.54 = 6.87 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAG

Scanning for motif occurrences 1.32 + 1.32 + 1.07 – 3.32 – 3.32 + 1.54 = -1.39 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAG

Summary DNA and protein motifs represent functionally or structurally important sequence elements. Motifs are typically represented using position-specific scoring matrices. A PSSM can be used to scan a given DNA or protein sequence to search for occurrences of the motif.