Sj�lander, Kimmen - Lawrence Berkeley National Laboratory & Department of Bioengineering, University of California at Berkeley

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Sj�lander, Kimmen - Lawrence Berkeley National Laboratory & Department of Bioengineering, University of California at Berkeley

insight progress NATURE | VOL 405 | 15 JUNE 2000 | www.nature.com 823
Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology
Predicting cellular localization Bioe C144/C244
Biology of Enzyme Active Sriram Sankararaman
Bioe C144L/C244L Lab 7: Functional Site Identification
Berkeley-India Roundtable Presents Bay AreaIndia
Nucleic Acids Research, 2007, Vol. 35, Web Server issue W27W32 doi:10.1093/nar/gkm325
Tutorial: Using hmmscore to select sequences and align them automatically.
Bioe/PMB C144L C244L Lab 6: Protein structure prediction
Lab 5: Constructing and analyzing multiple sequence alignments II (Answer Key)
Merck Irving S. Sigal Memorial Award The Merck Irving S. Sigal Memorial Award1
A functional role in plant defense mechanism and a predicted structure of the U-box domain combined
Functional site identification using evolutionary and 3D structure
BAliBASE 3.0: Latest Developments of the Multiple Sequence Alignment Benchmark
BIOINFORMATICS ORIGINAL PAPER Vol. 26 no. 5 2010, pages 617624
JMB--MS 422 Cust. Ref. No. CAM 502/94 [SGML] J. Mol. Biol. (1995) 247, 536540
BioE C144L/C244L MSA Construction and Analysis
Bioe 144/244 Introduction to Protein Informatics
Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient
Bioe C144L/C244L Lab 8: Transmembrane Prediction
Genome Biology 2006, 7:R83 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
Bioe C144/244 Intro to Protein Informatics
Structure prediction methods (2D and 3D)
Profile methods for homolog identification
ModBase, a database of annotated comparative protein structure models, and associated resources
OMICS A Journal of Integrative Biology Volume 10, Number 2, 2006
University of California, Berkeley REPORT ON PROGRESS IN CANDIDACY IN THE DOCTORAL PROGRAM
Phylogenomics, Orthologs, paralogs and public arguments
Protein structure Predictive methods and
Lab 6. Using HMM software. Answers to specific questions are in red, below. See the original lab for details on individual steps.
PPI data accuracy and interpretation
"Nothing in Biology Makes Sense Except in the Light of Evolution"
Bioe/PMB C144/244 Introduction to Protein Informatics
Tips for Lab 8 Lab 8 asks you to
Bioe144 projects Writing your project paper
SATCHMO: Simultaneous Alignment and Tree Construction using
Science & Engineering for Global Health 2012 CEND Research Fellowship
Arabidopsis Downy Mildew Resistance Gene RPP27 Encodes a Receptor-Like Protein Similar to CLAVATA2
Homework #2 -Due in class (hardcopy) Thursday, Sept 15. In this lab, you should learn to look up sequences at NCBI, use BLAST, and use
Protein structure Predictive methods and
J. Mol. Bioi. (1994) 235, 1501-1531 Hidden Markov Models in Computational Biology
Protein structure Predictive methods
BioE C144/244L Phylogenetic Tree Construction and Orthology Prediction
UNIT 19.5Basic Protein Sequence Analysis Protein sequence analysis can be performed from many perspectives and with a vast array
Protein structure Homology-based methods
Function Prediction Using Phylogenomics The status quo of functional annotation
Lab 7 answer key Part I: Submitting the query sequence to different structure prediction servers
Sequence, Structure, and Function Prediction for At1g10560.1 (U-box containing Arabidopsis thaliana protein)
Published online 11 October 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D943D946 doi:10.1093/nar/gkm798
Assessing methods for target-template alignment
Functional Analysis of Avr9/Cf-9 Rapidly Elicited Genes Identifies a Protein Kinase, ACIK1, That Is Essential for
Lab 4 Answer key Analysis of sequence gi|14587298 hypothetical protein [Oryza sativa (japonica cultivar-group)].
Berkeley PHOG: PhyloFacts Orthology Group Prediction Web Server Supplement 1: Description of the PHOG Algorithm
OPEN SOURCE DRUG DISCOVERY: FINDING A NICHE (OR MAYBE SEVERAL)
BIOINFORMATICS Vol. 20 no. 8 2004, pages 13091318
Nucleic Acids Research, 1994, Vol. 22, No. 22 4673-4680 CLUSTAL W: improving the sensitivity of progressive
Bioinformatics lab #1 Manual curation of two human amino acid sequences
Protein active sites, interaction
Bioe C144/244 Lecture notes for September 10, 2010
Original article Collaborative annotation of genes and
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families$
Getting started on your projects 1. Select a protein for analysis. We'll call this protein the "target." This protein should ideally meet all
Berkeley Phylogenomics Group Phylogenomic Analysis
BIOINFORMATICS Vol. 20 no. 8 2004, pages 13011308
In Proc. Twenty-Sixth Annual Hawaii International Conference on System Sciences. Eds. T.N Mudge, V. Milutinovic, and L. Hunter
BioMed Central Page 1 of 19
Subfamily HMMS in Functional Genomics D. Brown, N. Krishnamurthy, J.M. Dale, W. Christopher, and K. Sjlander
BioMed Central Page 1 of 11
Berkeley Phylogenomics Group Sequence "signal" guides the alignment
Homework #2 -Due in class (hardcopy) Thursday, Sept 15. In this lab, you should learn to look up sequences at NCBI, use BLAST, and use
Proteome Analysis of the Rice Etioplast METABOLIC AND REGULATORY NETWORKS AND NOVEL PROTEIN FUNCTIONS*S
5112-5120 Nucleic Acids Research, 1994, Vol. 22, No. 23 1994 Oxford University Press Stochastic context-free grammars for tRNA modeling
Constructing, viewing and editing alignments: Part I Belvu will refuse to read a file if there are repeated IDs, or if not all the lines in the file have the same
Predicting Protein Structure Using Hidden Markov Models
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models R.C. Edgar, K. Sjlander
Abriefintrotoinferringhomology BioeC144/244
UNIT 6.9Phylogenomic Inference of Protein Molecular Function
W390W395 Nucleic Acids Research, 2009, Vol. 37, Web Server issue Published online 13 May 2009 doi:10.1093/nar/gkp339
BIOINFORMATICS ORIGINAL PAPER Vol. 24 no. 21 2008, pages 24452452
Structure and function prediction of SGT1-like protein from Saccharomyces cerevisiae : An
BIOINFORMATICS Vol. 19 no. 11 2003, pages 14041411
"Nothing in Biology Makes Sense Except in the Light of Evolution"
Supplementary reading list from Understanding Bioinformatics
BIOINFORMATICS Vol. 20 no. 2 2004, pages 170179
Bioe C144/C244L Lab 5: Intro to PSI-BLAST and Hidden Markov Models
http://genomebiology.com/2001/2/2/comment/1002.1 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
Anopheles gambiae: A Source for Novel CARD-Containing Proteins e-mail: akeywu@uclink.berkeley.edu
Lab #2 (Part 2) Introduction to PyMol
insight progress NATURE | VOL 405 | 15 JUNE 2000 | www.nature.com 823
Functional Classification Using Phylogenomic Inference
Alignment of Group 1 sequences (Nck, Drk, Sem5 and Grb2) prior to editing NCK_HUMAN 1 -NPWYYGKVTRHQAEMALNERGH-EGDFLIRDSESSPNDFSVSLKAQGK----53
http://genomebiology.com/2001/2/8/interactions/1002.1 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
Hyperdimensional information network for data integration, navigation & community annotation
Bioe144 Lab 2 Introduction to PyMol
Guide to Pymol Download and Install PyMol
Protein-Protein Interaction Due November 5 by 4pm
Lab 3 Answer Key. Analysis of gi|482321|pir||A41784 tumor necrosis factor-alpha-induced protein B12 human (the
Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking
Genome Analysis Phylogenomic Analysis of the Receptor-Like Proteins of
http://genomebiology.com/2001/2/4/comment/1005.1 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
Automated protein function predictionthe genomic challenge
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree
James M. Berger UC Berkeley
RESEARCH ARTICLES From Endonucleases to Transcription Factors: Evolution of the
BioMed Central Page 1 of 14
Functional site identification using evolutionary and 3D structure
UNIT 19.5Basic Protein Sequence Analysis Protein sequence analysis can be performed from many perspectives and with a vast array
Aim: Structure analysis Databases: PDB
W84W89 Nucleic Acids Research, 2009, Vol. 37, Web Server issue Published online 12 May 2009 doi:10.1093/nar/gkp373
Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues as
UNIT 2.11Basic Protein Sequence Analysis Protein sequence analysis can be performed from many perspectives and with a vast array
Searching for MreB homologs in Agrobacterium
Berkeley Phylogenomics Group The devil's in the details!
Bioe144L Lab 2 Using PyMOL
Bioe C144/244 Introduction to Protein Informatics
Cataloguing and predicting protein-protein interaction
Bioe 144/244 syllabus Introduction to Protein Informatics
Bay Area-India TB Initiative Advancing the campaign against tuberculosis
Getting Started with SATCHMO Quick Start Guide
Message from ISCB Getting Started in Structural Phylogenomics
Predicting cellular localization Where a protein is localized is a critical
Berkeley PHOG: PhyloFacts Orthology Group Prediction Web Server Supplement 2: Detailed Description of Experiments
The SATCHMO Tutorial SATCHMO is a novel bioinformatics method that simultaneously constructs a phylogenetic tree and multiple
How to design experiments: Active site prediction
Lab 3. Using PSI-BLAST, the Taxonomy Report, the CDD analysis, and PFAM to look at proteins.
Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2
MHC Class II transactivator type I: a novel CARD domain containing protein
This work is supported by: The US DOE Systems Biology Knowledgebase,
UNIT 6.9Phylogenomic Inference of Protein Molecular Function
Lab 4: Multiple sequence alignment Download the alignment from PhyloFacts book: bpg002247, and save the alignment (Important: save as