Bioinformatica 20-10-2011-t3-scoring matrices
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This document provides an overview of topics to be covered in a bioinformatics course, including biological databases, sequence similarity scoring matrices, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, and other topics. A schedule is given listing the topics and dates. Background information is also provided on definitions, major bioinformatics databases, scoring matrices, and sequence alignments.
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Bioinformatica 20-10-2011-t3-scoring matrices
- 2. FBW 20-10-2011 Wim Van Criekinge
- 6. Anno 2002 Anno 2003
- 7. Anno 2004
- 8. Anno 2005
- 9. Anno 2006
- 10. Anno 2007
- 11. Anno 2009
- 12. Anno 2010 Anno 2010
- 13. Anno 2011
- 15. Identity The extent to which two (nucleotide or amino acid) sequences are invariant. Homology Similarity attributed to descent from a common ancestor. Definitions RBP: 26 RV K ENFDKARFS GTW YA MA KKDPEGLFLQDNIV A EFS V DE T GQMSATAKGRVRL L NN W D- 84 + K ++ + + GTW ++ MA + L + A V T + + L + W + glycodelin: 23 QT K QDLELPKLA GTW HS MA MA-TNNISLMATLK A PLR V HI T SLLPTPEDNLEIV L HR W EN 81
- 16. Orthologous Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. Paralogous Homologous sequences within a single species that arose by gene duplication. Definitions
- 18. fly GAKKVIISAP SAD.APM..F VCGVNLDAYK PDMKVVSNAS CTTNCLAPLA human GAKRVIISAP SAD.APM..F VMGVNHEKYD NSLKIISNAS CTTNCLAPLA plant GAKKVIISAP SAD.APM..F VVGVNEHTYQ PNMDIVSNAS CTTNCLAPLA bacterium GAKKVVMTGP SKDNTPM..F VKGANFDKY. AGQDIVSNAS CTTNCLAPLA yeast GAKKVVITAP SS.TAPM..F VMGVNEEKYT SDLKIVSNAS CTTNCLAPLA archaeon GADKVLISAP PKGDEPVKQL VYGVNHDEYD GE.DVVSNAS CTTNSITPVA fly KVINDNFEIV EGLMTTVHAT TATQKTVDGP SGKLWRDGRG AAQNIIPAST human KVIHDNFGIV EGLMTTVHAI TATQKTVDGP SGKLWRDGRG ALQNIIPAST plant KVVHEEFGIL EGLMTTVHAT TATQKTVDGP SMKDWRGGRG ASQNIIPSST bacterium KVINDNFGII EGLMTTVHAT TATQKTVDGP SHKDWRGGRG ASQNIIPSST yeast KVINDAFGIE EGLMTTVHSL TATQKTVDGP SHKDWRGGRT ASGNIIPSST archaeon KVLDEEFGIN AGQLTTVHAY TGSQNLMDGP NGKP.RRRRA AAENIIPTST fly GAAKAVGKVI PALNGKLTGM AFRVPTPNVS VVDLTVRLGK GASYDEIKAK human GAAKAVGKVI PELNGKLTGM AFRVPTANVS VVDLTCRLEK PAKYDDIKKV plant GAAKAVGKVL PELNGKLTGM AFRVPTSNVS VVDLTCRLEK GASYEDVKAA bacterium GAAKAVGKVL PELNGKLTGM AFRVPTPNVS VVDLTVRLEK AATYEQIKAA yeast GAAKAVGKVL PELQGKLTGM AFRVPTVDVS VVDLTVKLNK ETTYDEIKKV archaeon GAAQAATEVL PELEGKLDGM AIRVPVPNGS ITEFVVDLDD DVTESDVNAA Multiple sequence alignment of glyceraldehyde- 3-phsophate dehydrogenases
- 54. Other similarity scoring matrices might be constructed from any property of amino acids that can be quantified - partition coefficients between hydrophobic and hydrophilic phases - charge - molecular volume Unfortunately, …
- 56. Protein Eng. 1996 Jan;9(1):27-36.
- 65. Dayhoff’s PAM1 mutation probability matrix (Transition Matrix)
- 83. Dayhoff’s PAM1 mutation probability matrix (Transition Matrix)
- 85. PAM-Simulator
- 86. PAM-Simulator
- 91. 4 3 2 1 0 A brief history of time (BYA) Origin of life Origin of eukaryotes insects Fungi/animal Plant/animal Earliest fossils BYA
- 92. Margaret Dayhoff’s 34 protein superfamilies Protein PAMs per 100 million years Ig kappa chain 37 Kappa casein 33 Lactalbumin 27 Hemoglobin 12 Myoglobin 8.9 Insulin 4.4 Histone H4 0.10 Ubiquitin 0.00
- 96. BLOSUM ( BLO ck – SUM ) scoring DDNAAV DNAVDD NNVAVV Block = ungapped alignent Eg. Amino Acids D N V A a b c d e f 1 2 3 S = 3 sequences W = 6 aa N= (W*S*(S-1))/2 = 18 pairs
- 97. A. Observed pairs DDNAAV DNAVDD NNVAVV a b c d e f 1 2 3 D N A V D N A V 1 4 1 3 1 1 1 1 4 1 f f ij D N A V D N A V .056 .222 .056 .167 .056 .056 .056 .056 .222 .056 g ij /18 Relative frequency table Probability of obtaining a pair if randomly choosing pairs from block
- 98. B. Expected pairs A DDDDD NNNN AAAA VVVVV DDNAAV DNAVDD NNVAVV P i 5/18 4/18 4/18 5/18 P{Draw DN pair}= P{Draw D, then N or Draw M, then D} P{Draw DN pair}= P D P N + P N P D = 2 * (5/18)*(4/18) = .123 D N A V D N A V .077 .123 .154 .123 .049 .123 .099 .049 .123 .049 e ij Random rel. frequency table Probability of obtaining a pair of each amino acid drawn independently from block
- 105. Rat versus mouse RBP Rat versus bacterial lipocalin
- 114. Reduction of Dot Plot Noise Self alignment of ACCTGAGCTCACCTGAGTTA
- 116. Chromosome Y self comparison
Editor's Notes
- Mutation probability matrix for the evolutionary distance of 1 PAM (i.e., one Accepted Point Mutation per 100 amino acids). An element of this matrix, [Mij], gives the probability that the amino acid in column j will be replaced by the amino acid in row i after a given evolutionary interval, in this case 1 PAM. Thus, there is a 0.56% probability that Asp will be replaced by Glu. To simplify the appearance, the elements are shown multiplied by 10,000. (Adapted from Figure 82. Atlas of Protein Sequence and Structure, Suppl 3, 1978, M.O. Dayhoff, ed. National Biomedical Research Foundation, 1979.)