'Psi blast' diaporamas de présentation

Protein structure prediction

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Advanced BLAST Searching

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GROUP MEMBERS: MUHAMMAD KHAIRULANWAR IZZAT BIN HUSSIN AC100076

GROUP MEMBERS: MUHAMMAD KHAIRULANWAR IZZAT BIN HUSSIN AC100076 MURNIYANTI BINTI MALIK AC100078 NG SHEE TING AC100079 SCHEE XIN LIN AC100086 AW MEI YEE AC100062. INTRODUCTION. @Ng Shee Ting. INTRODUCTION(cont..).

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Machine learning methods for protein analyses

Machine learning methods for protein analyses. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington. Outline. Remote homology detection from protein sequences Identifying proteins from tandem mass spectra

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Outline

PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis. Outline. Introduction Protein Subcellular Localization Document Classification PSLDoc Term and its weighting scheme Feature Reduction SVM learning

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Introduction to Bioinformatics

Introduction to Bioinformatics. Lecture 12 : Iterative h omology searching and Protein Structure-Function Relationships Centre for Integrative Bioinformatics VU (IBIVU). PSI ( Position Specific Iterated ) BLAST. basic idea use results from BLAST query to construct a profile matrix

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Prologue

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Protein Classification

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Profiles and Fuzzy K-Nearest Neighbor Algorithm for Protein Secondary Structure Prediction

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Multiple Sequence Alignments Advanced BLAST searches

Multiple Sequence Alignments Advanced BLAST searches. June 17, 2014. Topics. Overview of MSA MSA methods Practical aspects MSA to Profiles PSI- BLAST PHI-BLAST. Overview of MSA. Alignment of ? 3 sequences to bring as many similar characters into register as possible

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Introduction to bioinformatics 2007 Lecture 13

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Introduction to bioinformatics 2007 Lecture 13. Iterative h omology searching,. PSI ( Position Specific Iterated ) BLAST. basic idea

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Pairwise Sequence Alignment Exercise 2

Pairwise Sequence Alignment Exercise 2. Motivation.

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Classifying the protein universe

Synapse-Associated Protein 97. Classifying the protein universe. Wu et al, 2002. EMBO J 19:5740-5751. Domain Analysis and Protein Families. Introduction What are protein families? Protein families Description & Definition Motifs and Profiles The modular architecture of proteins

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Hacking the Genome - Designer Proteins, Elite Organisms, and You

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Bioinformatics

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Fold Recognition

Fold Recognition. Ole Lund, Associate professor, CBS. Fold recognition. Find template for modeling 1st step in comparative modeling Can be used to predict function. Template identification. Search with sequence Blast against proteins with known structure Psi-Blast against all proteins

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Genome Annotation Continued

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Introduction to Bioinformatics - Tutorial no. 8

Introduction to Bioinformatics - Tutorial no. 8. Predicting protein structure PSI-BLAST. PHDsec and PSIpred. PHDsec Rost & Sander, 1993 Based on sequence family alignments PSIpred Jones, 1999 Based on PSI-BLAST profiles Both consider long-range interactions. PSIpred Input.

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HSP-HMMER vs MPI-HMMER & parallelization of PSI-BLAST

HSP-HMMER vs MPI-HMMER & parallelization of PSI-BLAST. Christian Halloy halloy@jics.utk.edu April 23, 2009. HMMER, PFAM, and PSI-BLAST. If you BLAST a protein sequence (or a translated nucleotide sequence) BLAST will look for known domains in the query sequence.

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BLAST:

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