'Protein families' diaporamas de présentation

Protein function and classification

Protein function and classification . Hsin -Yu Chang www.ebi.ac.uk. Classifying proteins into families and identifying protein homologues can help scientists to characterise unknown proteins . .

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Web site: bioinfo.weizmann.ac.il/ws Mailing list: bioinfo.weizmann.ac.il/announce Contact: Vered.Caspi@weizmann.ac.il

Web site: http://bioinfo.weizmann.ac.il/ws Mailing list: http://bioinfo.weizmann.ac.il/announce Contact: Vered.Caspi@weizmann.ac.il. Genomic Databases and Analysis Tools 09:00-09:45 Vered Chalifa-Caspi Genomic Databases: from primary DNA sequence to gene function 09:45-11:00

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Applications of HMMs

Applications of HMMs. Yves Moreau 2003-2004. Overview. Profile HMMs Estimation Database search Alignment Gene finding Elements of gene prediction Prokaryotes vs. eukaryotes Gene prediction by homology GENSCAN. GGWWRGdy.ggkkqLWFPSNYV IGWLNGynettgerGDFPGTYV PNWWEGql..nnrrGIFPSNYV

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Large-scale genome projects

Strategy. Libraries. Sequencing. Assembly. Closure. Annotation. Release. Large-scale genome projects. Sequencing DNA molecules in the Mb size range All strategies employ the same underlying principles: Random Shotgun sequencing. Genomic DNA. Shearing/Sonication.

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Annotation Presentation Week 6

Annotation Presentation Week 6. Structure-based Evidence for Function (TIGRfam, Pfam and PDB). TIGRfams are protein families categorized by functional role. Concept: HMMs. A concrete example of an HMM:.

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Pros and cones of genomic mutations

Pros and cones of genomic mutations. February 24 th , 2011 Alexei Fedorov Bioinformatics Program, University of Toledo. This book explores the weaknesses of Darwinian theory from the perspective of someone who has been at the cutting-edge of genetic research. .

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Molecular biology databases

Molecular biology databases. Based on Chapter 2 of Post-genome Informatics by Minoru Kanehisa, Oxford University Press, 2000 2.1 History 2.2 Information Technology

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Sequence Similarity

Sequence Similarity. x i. ?. x i. y j. MATCH. PROBCONS: Probabilistic Consistency-based Multiple Alignment of Proteins. INSERT X. INSERT Y. ?. y j. x i. y j. MATCH. INSERT X. INSERT Y. x i. ?. ?. y j. A pair-HMM model of pairwise alignment.

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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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BioPathways SIG, July.29.2004

BioPathways SIG, July.29.2004 . Networks in Biology. Molecular interaction and similarity networks are vital for understanding gene function in biology How does my gene of unknown function relate to a known gene?

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Bioinformatics

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Investigating Genomes with Ensembl

Investigating Genomes with Ensembl. Drs. Bert Overduin and Giulietta Spudich. Overview of the day. Introduction and website walk-through Hands-on exercises (the browser) Tea/Coffee Introduction to BioMart Hands-on exercises (BioMart) Lunch Determining the gene set

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Multiple Alignments Motifs/Profiles

Multiple Alignments Motifs/Profiles. What is multiple alignment? HOW does one do this? WHY does one do this? What do we mean by a motif or profile?. Prev. reading: Ch 1-5 Assigned reading: Ch 6.4, 6.5, 6.6. BIO520 Bioinformatics Jim Lund. Information from Alignments.

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Protein structures

Protein structures. Haixu Tang School of Inforamtics. A covalent peptide bond . Protein conformation is specified by tts Amino Acid sequence . Steric interactions Weak non-covalent bonds hydrogen bonds ionic bonds van der Waals attractions Hydrophobic interaction

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Protein Structure

Protein Structure. July 1, 2007

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CRISPR-associated Proteins

CRISPR-associated Proteins . Sarah Pyfrom sapyfrom@davidson.edu. Research Questions. What Cas-proteins does our species share with the 10 other species we chose to study? If so, how do they compare? How do Cas-proteins function in relation to CRISPR units? [Edit]:

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Comparative Genomics in Basidiomycetes - Analyzing multigene families

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Comparing Data from MD simulations and X-ray Crystallography

Comparing Data from MD simulations and X-ray Crystallography. What can we compare? 3D shapes (RMSD) Atomic motions (B-value, RMSF) Solvent accessibilities (SASA). Tools for Analyzing Protein 3D Structures.

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Acknowledgements

Abbreviations. DBD: DNA Binding Domain ; TF: Transcription Factor ; A: Activator ; R: Repressor ; D: Dual Regulator ; U: Unknown regulatory function ; RNAP: RNA Polymerase. Acknowledgements.

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Spectral matching identifies peptides by comparing spectra with libraries of identified spectra

D1. D2. D3. D4. I0. I1. I2. I4. I3. Begin. b1. y1. b2. y2. End. HMMatch : Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. US HUPO.

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