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Position-Specific Iterated BLAST (PSI-BLAST)

Position-Specific Iterated BLAST (PSI-BLAST). CISC 4020 Bioinformatics Spring 2012 Department of Computer and Information Science. Position specific iterated BLAST: PSI-BLAST.

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Position-Specific Iterated BLAST (PSI-BLAST)

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  1. Position-Specific Iterated BLAST(PSI-BLAST) CISC 4020 Bioinformatics Spring 2012 Department of Computer and Information Science

  2. Position specific iterated BLAST: PSI-BLAST • Many homologous proteins share only limited sequence identity. They may adopt the same 3-D structures, but in pairwise alignments they may have no apparent similarity. • Position specific iterated BLAST is a specialized kind of BLAST search that is often more sensitive than a regular BLAST search. CISC 4020 Bioinformatics

  3. Position specific iterated BLAST: PSI-BLAST • The purpose of PSI-BLAST is to look deeper into the database for matches to your query protein sequence by employing a scoring matrix that is customized to your query. • PSI-BLAST is performed in five steps. CISC 4020 Bioinformatics

  4. Searching Steps • Select a query and search it against a protein database. • PSI-BLAST constructs a multiple sequence alignment then creates a “profile” or specialized position-specific scoring matrix (PSSM). • The key idea is that the aligned residues at each position of the multiple sequence alignment provide information about the unique profile of accepted mutations in the query and its nearest database matches. CISC 4020 Bioinformatics

  5. Inspect the blastp output to identify empirical “rules” regarding amino acids tolerated at each position R,I,K C D,E,T K,R,T N,L,Y,G CISC 4020 Bioinformatics

  6. Position Specific Scoring Matrix (PSSM) • A PAM or BLOSUM matrix describes the likelihood that one amino acid will be substituted for another, based on a statistical analysis of thousands of proteins. • The PSSM is created specifically for the protein query of the initial PSI-BLAST search (a standard blastp search with some amino acid substitution matrix such as BLOSUM62). Substitutions that may be unique to the particular group of proteins are studied. CISC 4020 Bioinformatics

  7. Position Specific Scoring Matrix (PSSM) • For a query of length L, PSI-BLAST generates a PSSM of dimension L X 20. • Redundant sequences (having at least 94% identity) are eliminated to ensure that a group of very closely related sequences will not overly bias the construction of the PSSM. • The same gap scores are applied as in blastp. CISC 4020 Bioinformatics

  8. A R N D C Q E G H I L K M F P S T W Y V 1 M -1 -2 -2 -3 -2 -1 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 2 K -1 1 0 1 -4 2 4 -2 0 -3 -3 3 -2 -4 -1 0 -1 -3 -2 -3 3 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 4 V 0 -3 -3 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -1 4 5 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 6 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 7 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 8 L -1 -3 -3 -4 -1 -3 -3 -4 -3 2 2 -3 1 3 -3 -2 -1 -2 0 3 9 L -1 -3 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 2 10 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 11 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 12 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 13 W -2 -3 -4 -4 -2 -2 -3 -4 -3 1 4 -3 2 1 -3 -3 -2 7 0 0 14 A 3 -2 -1 -2 -1 -1 -2 4 -2 -2 -2 -1 -2 -3 -1 1 -1 -3 -3 -1 15 A 2 -1 0 -1 -2 2 0 2 -1 -3 -3 0 -2 -3 -1 3 0 -3 -2 -2 16 A 4 -2 -1 -2 -1 -1 -1 3 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 -1 ... 37 S 2 -1 0 -1 -1 0 0 0 -1 -2 -3 0 -2 -3 -1 4 1 -3 -2 -2 38 G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 39 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 40 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 41 Y -2 -2 -2 -3 -3 -2 -2 -3 2 -2 -1 -2 -1 3 -3 -2 -2 2 7 -1 42 A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 20 amino acids all the amino acids from position 1 to the end of your PSI-BLAST query protein CISC 4020 Bioinformatics

  9. A R N D C Q E G H I L K M F P S T W Y V 1 M -1 -2 -2 -3 -2 -1 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 2 K -1 1 0 1 -4 2 4 -2 0 -3 -3 3 -2 -4 -1 0 -1 -3 -2 -3 3 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 4 V 0 -3 -3 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -1 4 5 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 6 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 7 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 8 L -1 -3 -3 -4 -1 -3 -3 -4 -3 2 2 -3 1 3 -3 -2 -1 -2 0 3 9 L -1 -3 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 2 10 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 11 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 12 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 13 W -2 -3 -4 -4 -2 -2 -3 -4 -3 1 4 -3 2 1 -3 -3 -2 7 0 0 14 A 3 -2 -1 -2 -1 -1 -2 4 -2 -2 -2 -1 -2 -3 -1 1 -1 -3 -3 -1 15 A 2 -1 0 -1 -2 2 0 2 -1 -3 -3 0 -2 -3 -1 3 0 -3 -2 -2 16 A 4 -2 -1 -2 -1 -1 -1 3 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 -1 ... 37 S 2 -1 0 -1 -1 0 0 0 -1 -2 -3 0 -2 -3 -1 4 1 -3 -2 -2 38 G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 39 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 40 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 41 Y -2 -2 -2 -3 -3 -2 -2 -3 2 -2 -1 -2 -1 3 -3 -2 -2 2 7 -1 42 A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 CISC 4020 Bioinformatics

  10. A R N D C Q E G H I L K M F P S T W Y V 1 M -1 -2 -2 -3 -2 -1 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 2 K -1 1 0 1 -4 2 4 -2 0 -3 -3 3 -2 -4 -1 0 -1 -3 -2 -3 3 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 4 V 0 -3 -3 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -1 4 5 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 6 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 7 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 8 L -1 -3 -3 -4 -1 -3 -3 -4 -3 2 2 -3 1 3 -3 -2 -1 -2 0 3 9 L -1 -3 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 2 10 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 11 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 12 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 13 W -2 -3 -4 -4 -2 -2 -3 -4 -3 1 4 -3 2 1 -3 -3 -2 7 0 0 14 A 3 -2 -1 -2 -1 -1 -2 4 -2 -2 -2 -1 -2 -3 -1 1 -1 -3 -3 -1 15 A 2 -1 0 -1 -2 2 0 2 -1 -3 -3 0 -2 -3 -1 3 0 -3 -2 -2 16 A 4 -2 -1 -2 -1 -1 -1 3 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 -1 ... 37 S 2 -1 0 -1 -1 0 0 0 -1 -2 -3 0 -2 -3 -1 4 1 -3 -2 -2 38 G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 39 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 40 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 41 Y -2 -2 -2 -3 -3 -2 -2 -3 2 -2 -1 -2 -1 3 -3 -2 -2 2 7 -1 42 A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 note that a given amino acid (such as alanine) in your query protein can receive different scores for matching alanine—depending on the position in the protein CISC 4020 Bioinformatics

  11. A R N D C Q E G H I L K M F P S T W Y V 1 M -1 -2 -2 -3 -2 -1 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 2 K -1 1 0 1 -4 2 4 -2 0 -3 -3 3 -2 -4 -1 0 -1 -3 -2 -3 3 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 4 V 0 -3 -3 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -1 4 5 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 6 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 7 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 8 L -1 -3 -3 -4 -1 -3 -3 -4 -3 2 2 -3 1 3 -3 -2 -1 -2 0 3 9 L -1 -3 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 2 10 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 11 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 12 A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 13 W -2 -3 -4 -4 -2 -2 -3 -4 -3 1 4 -3 2 1 -3 -3 -2 7 0 0 14 A 3 -2 -1 -2 -1 -1 -2 4 -2 -2 -2 -1 -2 -3 -1 1 -1 -3 -3 -1 15 A 2 -1 0 -1 -2 2 0 2 -1 -3 -3 0 -2 -3 -1 3 0 -3 -2 -2 16 A 4 -2 -1 -2 -1 -1 -1 3 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 -1 ... 37 S 2 -1 0 -1 -1 0 0 0 -1 -2 -3 0 -2 -3 -1 4 1 -3 -2 -2 38 G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 39 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 40 W -3 -3 -4 -5 -3 -2 -3 -3 -3 -3 -2 -3 -2 1 -4 -3 -3 12 2 -3 41 Y -2 -2 -2 -3 -3 -2 -2 -3 2 -2 -1 -2 -1 3 -3 -2 -2 2 7 -1 42 A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 note that a given amino acid (such as tryptophan) in your query protein can receive different scores for matching tryptophan—depending on the position in the protein CISC 4020 Bioinformatics

  12. Searching Steps • Select a query and search it against a protein database. • PSI-BLAST constructs a multiple sequence alignment then creates a “profile” or specialized position-specific scoring matrix (PSSM). • The PSSM is used as a query against the database. • PSI-BLAST estimates statistical significance (E values). CISC 4020 Bioinformatics

  13. CISC 4020 Bioinformatics

  14. Searching Steps • Select a query and search it against a protein database. • PSI-BLAST constructs a multiple sequence alignment then creates a “profile” or specialized position-specific scoring matrix (PSSM). • The PSSM is used as a query against the database. • PSI-BLAST estimates statistical significance (E values). • Repeat steps 3 and 4 iteratively, typically 5 times. At each new search, a new profile is used as the query. CISC 4020 Bioinformatics

  15. Results of a PSI-BLAST search # hits Iteration# hits> threshold 1 104 49 2 173 96 3 236 178 4 301 240 5 344 283 6 342 298 7 378 310 8 382 320 CISC 4020 Bioinformatics

  16. PSI-BLAST search: human RBP versus RefSeq CISC 4020 Bioinformatics

  17. PSI-BLAST search: human RBP versus RefSeq, iteration 1 CISC 4020 Bioinformatics

  18. CISC 4020 Bioinformatics

  19. PSI-BLAST search: human RBP versus RefSeq, iteration 2 CISC 4020 Bioinformatics

  20. CISC 4020 Bioinformatics

  21. PSI-BLAST search: human RBP versus RefSeq, iteration 3 CISC 4020 Bioinformatics

  22. PSI-BLAST search: human RBP versus RefSeq, iteration 4 CISC 4020 Bioinformatics

  23. The universe of lipocalins (each dot is a protein) retinol-binding protein odorant-binding protein apolipoprotein D Fig. 5.7 Page 151 CISC 4020 Bioinformatics

  24. Scoring matrices let you focus on the big (or small) picture retinol-binding protein Fig. 5.7 Page 151 your RBP query CISC 4020 Bioinformatics

  25. Scoring matrices let you focus on the big (or small) picture PAM250 PAM30 retinol-binding protein retinol-binding protein Blosum80 Blosum45 Fig. 5.7 Page 151 CISC 4020 Bioinformatics

  26. PSI-BLAST generates scoring matrices more powerful than PAM or BLOSUM retinol-binding protein retinol-binding protein Fig. 5.7 Page 151 CISC 4020 Bioinformatics

  27. Advantage of PSI-BLAST • In a PSI-BLAST search, a PSSM generates a scoring system that is specific to the group of matches detected using the initial query sequence. This customized matrix enables the search results to include more distantly related homologs. • The fundamental limitation in standard BLAST search sensitivity is the reliance on standard PAM or BLOSUM scoring matrices. CISC 4020 Bioinformatics

  28. PSI-BLAST: performance assessment • Evaluate PSI-BLAST results using a database in which protein structures have been solved and all proteins in a group share < 25% amino acid identity. CISC 4020 Bioinformatics

  29. PSI-BLAST: the problem of corruption PSI-BLAST is useful to detect statistically weak but Biologically meaningful relationships between proteins. The main source of false positives is the spurious amplification of sequences not related to the query. Once even a single spurious protein is included in a PSI-BLAST search above threshold, it will not go away. CISC 4020 Bioinformatics Page 152

  30. PSI-BLAST: the problem of corruption Corruption is defined as the presence of at least one false positive alignment with an E value < 10-4 after five iterations. Three approaches to stopping corruption: [1] Apply filtering of biased composition regions [2] Adjust E value from 0.005 (default) to a lower value such as E = 0.0001. [3] Visually inspect the output from each iteration. Remove suspicious hits by unchecking the box. CISC 4020 Bioinformatics Page 152

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