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CMU BSC 03510 - Computational Biology, Part 5
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Computational Biology, Part 5 Multiple Sequence AlignmentMultiple Sequence AlignmentPowerPoint PresentationSlide 4Pairwise Multiple Sequence Alignment Example 2Slide 6Slide 7Slide 8“True” Multiple Sequence AlignmentHow do we score a multiple-sequence alignment?Slide 11Scoring Global Multiple Sequence AlignmentsAlternative scoring approachesMultiple Sequence Alignment programsMSASlide 16Weighting scores to de-emphasis distant relativesSlide 18CLUSTALWSlide 20Slide 21ClustalW Guide TreeClustalW graphical display (partial)ClustalW interleaved fileClustalW sequential fileGlobal vs. LocalMultiple Alignment ServersReading for next classComputational Biology, Part 5Multiple Sequence AlignmentComputational Biology, Part 5Multiple Sequence AlignmentRobert F. MurphyRobert F. MurphyCopyright Copyright  1996-2006. 1996-2006.All rights reserved.All rights reserved.Multiple Sequence AlignmentMultiple Sequence AlignmentGoal: Goal: Create best possible “overall” Create best possible “overall” alignment of a family of sequences (more alignment of a family of sequences (more than two)than two)First approximation: First approximation: Align all of the Align all of the members members pairwise pairwise with with oneone of the members of the membersDescription ListSearch Analysis for Sequence: A23035 Matrix: pam250 matrixSearch from 1 to 451 where origin = 1 Score Region from 1 to 451Date: February 20,1997 Maximum possible score: 2265Time: 00:48:27 Database: UserFolder: tubulinsSequence Opt. Init. Description 1. A23035 2265 2265 Tubulin alpha chain - Human 2. A25873 2193 2176 Tubulin alpha chain - Human 3. UBUTA 1995 1995 Tubulin alpha chain - Trypanosoma brucei rhodesiense 4. A25601 1952 1948 Tubulin alpha chain - Slime mold (Physarum polycephalum) 5. UBUTB 1058 754 Tubulin beta chain - Trypanosoma brucei rhodesiense 6. A29141 1051 755 Tubulin beta chain - Chlamydomonas reinhardtii 7. A26561 1050 773 Tubulin beta chain - Human 8. UBPGB 1044 765 Tubulin beta chain - Pig 9. UBCHB 1043 765 Tubulin beta chain, embryonic - Chicken 10. A25377 1022 762 Tubulin beta chain - Neurospora crassa 11. UBBYB 1002 699 Tubulin beta chain - Yeast (Saccharomyces cerevisiae) 12. UBURAL 826 826 Tubulin alpha chain - Sea urchin (Lytechinus pictus) (fragment) 13. A25342 532 361 Tubulin beta chain - Slime mold (Physarum polycephalum) 14. UBURB 354 182 Tubulin beta chain - Sea urchin (Lytechinus pictus) (fragment)Aligned Sequence Description List for TubulinsAligned Sequence Description List for TubulinsSearch Analysis for Sequence: A23035 Matrix: pam250 matrixSearch from 1 to 451 where origin = 1 Score Region from 1 to 451Date: February 20,1997 Maximum possible score: 2265Time: 00:48:27Database: UserFolder: tubulins 1. A23035 2265 2. A25873 2193 3. UBUTA 1995 4. A25601 1952 5. UBUTB 1058 6. A29141 1051 7. A26561 1050 8. UBPGB 1044 9. UBCHB 1043 10. A25377 1022 11. UBBYB 1002 12. UBURAL 826 13. A25342 532 14. UBURB 3545050100100150150200200250250300300350350400400450450Aligned Sequence Map for TubulinsAligned Sequence Map for TubulinsPairwise Multiple Sequence Alignment Example 2Pairwise Multiple Sequence Alignment Example 2Input: Input: Just three tubulinsJust three tubulinsTask: Task: Compare results using different query Compare results using different query sequences and examine aligned sequence sequences and examine aligned sequence listing for differenceslisting for differencesAlignment ListSearch Analysis for Sequence: A23035 Matrix: pam250 matrixSearch from 1 to 451 where origin = 1 Score Region from 1 to 451Date: February 20,1997 Maximum possible score: 2265Time: 00:51:34 Database: UserFolder: subset of tubulins 10 20 30 40 50 60 * * * * * * * * * * * *A23035 MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK | | | | | | 1. A23035 10 20 30 40 50 60[ 2265 ] MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK> ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^A23035 MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK | | | | | | 2. A25601 10 20 30 40 50 60[ 1952 ] MREvISIHiG QAGtQvGNAC WELYCLEHGI QPDGQMPSDK svGyGDDaFN TFFSETGAGK> ^^^v^^^^^^ ^^^-^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^v^^^^^^ ^^^^^^^^^^A23035 MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK | | | | | | 3. UBUTB 10 20 30 40 | 50 |[ 1058 ] MREivcvqaG QcGnQIGskf WEvisdEHGv dPtGtyqgDs dl--qleriN vyFdEatgGr> ^^^v^-^^-^ ^v^v^^^^vv ^^^v-v^^^^ ^^-^vv-^^- -^ vv^-^^ -^^-^^-^^^A23035 MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGKAlignment ListSearch Analysis for Sequence: A25601 Matrix: pam250 matrixSearch from 1 to 450 where origin = 1 Score Region from 1 to 450Date: February 20,1997 Maximum possible score: 2161Time: 00:52:46 Database: UserFolder: subset of tubulins 10 20 30 40 50 60 * * * * * * * * * * * *A25601 MREVISIHIG QAGTQVGNAC WELYCLEHGI QPDGQMPSDK SVGYGDDAFN TFFSETGAGK | | | | | | 1. A25601 10 20 30 40 50 60[ 2161 ] MREVISIHIG QAGTQVGNAC WELYCLEHGI QPDGQMPSDK SVGYGDDAFN TFFSETGAGK> ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^A25601 MREVISIHIG QAGTQVGNAC WELYCLEHGI QPDGQMPSDK SVGYGDDAFN TFFSETGAGK | | | | | | 2. A23035 10 20 30 40 50 60[ 1948 ] MREcISIHvG QAGvQiGNAC WELYCLEHGI QPDGQMPSDK tiGgGDDsFN TFFSETGAGK> ^^^v^^^^^^ ^^^-^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ ^^^v^^^^^^ ^^^^^^^^^^A25601 MREVISIHIG QAGTQVGNAC


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