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Speeding the Database Searches and Sequence Alignments with Multi-Motif PHI-BLAST

Speeding the Database Searches and Sequence Alignments with Multi-Motif PHI-BLAST. Nitin Bhardwaj, Dept. of Chemical Engineering, IIT Bombay. National Center For Biological Sciences, (NCBS) Bangalore A unit of TATA Institute of Fundamental Research (TIFR). What is Sequence Alignment ?.

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Speeding the Database Searches and Sequence Alignments with Multi-Motif PHI-BLAST

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  1. Speeding the Database Searches and Sequence Alignments with Multi-Motif PHI-BLAST Nitin Bhardwaj, Dept. of Chemical Engineering, IIT Bombay.

  2. National Center For Biological Sciences, (NCBS)Bangalore A unit of TATA Institute of Fundamental Research (TIFR)

  3. What is Sequence Alignment ? Why make Sequence Alignments ? To detect: Structural & Functional Relationship The process of lining up two or more sequences to achieve maximal levels of similarity Evolutionary Relationship

  4. Entire Sequence Some Basic Terms Local Alignment Restricted to regions of identity and strong similarity Query Sequence Global Alignment The sequence of interest Subject Sequence The other one

  5. And…. Motif: A short conserved region of a sequence Hits: Sequences picked up from the database True Positive False Negative False Positive Scoring Matrices: to score a match/mismatch True Negative

  6. What after alignment ? Sort the aligned sequences in the order of their decreasing scores Calculate the score of the alignment Go ahead with your analysis to find out the relationships/similarities

  7. Pattern-Hit Initiated Basic Local Alignment Search Tool (PHI-BLAST) Aligns the query sequence with all the seqs which have the motif Brings out a score for each seq Takes a query seq, a motif, a database to search into Reports all the seqs which have the score above a particular thresh-hold value sorted in the order of the score

  8. A Typical PHI-BLAST Output 1occurrence(s) of pattern in query pattern [RA][C][ACDEFGHIKLMNPQRSTVWY][C] at position 3 of query sequence Significant matches for pattern occurrence 1 at position 3 Score E Value(bits) pdb|1ILP|A Chain A, Cxcr-1 N-Terminal Peptide Bound To Interleuk... 128 2e-37 pdb|1QE6|D Chain D, Interleukin-8 With An Added Disulfide Betwee... 121 2e-35 pdb|1ICW|A Chain A, Interleukin-8, Mutant With Glu 38 Replaced B... 121 3e-35 pdb|1ROD|A Chain A, Chimeric Protein Of Interleukin 8 And Human ... 98 2e-28 pdb|1TVX|B Chain B, Neutrophil Activating Peptide-2 Variant Form... 50 6e-14 pdb|1NAP|A Chain A, Mol_id: 1; Molecule: Neutrophil Activating P... 50 6e-14 pdb|1MSG|A Chain A, Human Melanoma Growth Stimulatory Activity (... 48 3e-13 pdb|1MGS|A Chain A, Human Melanoma Growth Stimulating Activity (... 48 3e-13 pdb|1QNK|A Chain A, Truncated Human Grob[5-73], Nmr, 20 Structur... 47 5e-13 pdb|1MI2|A Chain A, Solution Structure Of Murine Macrophage Infl... 46 1e-12

  9. Strategy behind PHI-BLAST Extension in both directions with local alignment Calculate the score for the alignment Location of motifs in the seqs Motif (Query) Motif (Subject)

  10. Problems with PHI-BLAST Consequently, no space for attaching any weightage to any motif No control on the specificity of the program Only one motif as input so no of runs required thus increasing the time No parallel comparison possible

  11. The Solution(s) !!! RANKED MOTIF PHI-BLAST (RMPB) MULTI – MOTIF PHI-BLAST (MMPB)

  12. Takes a query seq, any no of motifs, a database to search into Multi-Motif PHI-BLAST Aligns the query sequence with all the seqs which have a min no of motif(s) Brings out a score for each seq Reports all the seqs which have the score above a particular thresh-hold value sorted in the order of the score

  13. Location of motifs in the two seqs Strategy behind MMPB Extension in both directions with local alignment and the part in between with global alignment Calculate the score for the alignment Query Motif 1 Motif 2 (Global) (Local) (Global) Motif 1 Subject Motif 2

  14. il8 Macrophage Inflammatory 1beta (the middle columns correspond to PHI-BLAST(e=1) And the last one correspond to MMPB Comparison of Results

  15. il8 (1ikl) Interleukin-8

  16. 4helud (1bbh) Cytochrome $c (prime)

  17. 4helud (256b) Cytochrome $b502

  18. Flav (1ord) Orthinine Decarboxylase

  19. Flav (1cus)Cutinase

  20. Takes a query seq, a number of motifs in the order of their ranks, and a database to search into Ranked Motif PHI-BLAST Aligns the query sequence with all the seqs which have the min no of highest ranked motifs Brings out a score for each seq Reports all the seqs which have the score above a particular thresh-hold value sorted in the order of the score

  21. Comparison of resultsResults for il8 (1hum) Macrophage Inflammatory 1beta the unmarked columns correspond to RMPB with at least 3 & 2

  22. il8 (1ikl) Interleukin-8

  23. The problems are solved !!!! Only one run required for any number of motifs so less time Space for attaching weightage to the motifs via their ranks Space for multiple motifs as input A deeper analysis possible

  24. That’s All & Thanks to All of You

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