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New Parallel Scheme of HMMer PFAM PowerPoint PPT Presentation
New Parallel Scheme of HMMer PFAM - New Parallel Scheme of HMMer PFAM. Weirong Zhu. Niu Yanwei. HMMPFAM INPUT. Profile n. Profile n- 1 ... Each slave node is only responsible for one part profiles ...
New Parallel Scheme of HMMer PFAM. Weirong Zhu. Niu Yanwei. HMMPFAM INPUT. Profile n. Profile n- 1 ... Each slave node is only responsible for one part profiles ...
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HIMMER PFAM algorithm and parallel schemes PowerPoint PPT Presentation
HIMMER PFAM algorithm and parallel schemes - 256 dual-CPU Pentium III 500 MHz Computing Nodes with 512 MB of RAM and 9G of local disk. ... data parallel, computation intensive, global reduction and barrier ...
256 dual-CPU Pentium III 500 MHz Computing Nodes with 512 MB of RAM and 9G of local disk. ... data parallel, computation intensive, global reduction and barrier ...
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Expansion of the pfam 01617 family of major outer membrane proteins in Ehrlichia sp' A' Findley, C' PowerPoint PPT Presentation
Expansion of the pfam 01617 family of major outer membrane proteins in Ehrlichia sp' A' Findley, C' - have complex protein structure in the outer membrane ... differential expression between mammalian & arthropod host. OMP1-X. Msp4 303525. OMP1 ...
have complex protein structure in the outer membrane ... differential expression between mammalian & arthropod host. OMP1-X. Msp4 303525. OMP1 ...
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Orthology%20Analysis PowerPoint PPT Presentation
Orthology%20Analysis - ... OrthoMCL OrthoMCL (blast) proteomes HOPS Orthostrapper (tree) Pfam RIO (tree) Pfam TOGA/EGO COGs (blast) TIGR gene index COGs / KOGs COGs (blast) ...
... OrthoMCL OrthoMCL (blast) proteomes HOPS Orthostrapper (tree) Pfam RIO (tree) Pfam TOGA/EGO COGs (blast) TIGR gene index COGs / KOGs COGs (blast) ...
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T-COFFEE, a novel method for Multiple Sequence Alignments PowerPoint PPT Presentation
T-COFFEE, a novel method for Multiple Sequence Alignments - T-COFFEE, a novel method for Multiple Sequence Alignments C dric Notredame WHO ? WHO USES T-Coffee ? Dali Domain Dictionnary Pfam SwissProt WHO Makes T-Coffee ?
T-COFFEE, a novel method for Multiple Sequence Alignments C dric Notredame WHO ? WHO USES T-Coffee ? Dali Domain Dictionnary Pfam SwissProt WHO Makes T-Coffee ?
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Sequence%20databases%20and%20retrieval%20systems PowerPoint PPT Presentation
Sequence%20databases%20and%20retrieval%20systems - High-quality annotations: Systematic control by a team of annotators. ... InterPro unifies PROSITE, PRINTS, Profile, ProDom, Pfam, SMART, and TIGRFam. InterPro ...
High-quality annotations: Systematic control by a team of annotators. ... InterPro unifies PROSITE, PRINTS, Profile, ProDom, Pfam, SMART, and TIGRFam. InterPro ...
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1. intermediate proteins. PowerPoint PPT Presentation
1. intermediate proteins. - ???? ??? ????? ??? ?????? ????? ?????? (MSA) ??????? ?????. ... ??????? ?????? PSI-BLAST ?????? ????????? ??????? ?- Pfam, SCOP, COG ??????. ...
???? ??? ????? ??? ?????? ????? ?????? (MSA) ??????? ?????. ... ??????? ?????? PSI-BLAST ?????? ????????? ??????? ?- Pfam, SCOP, COG ??????. ...
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PIRSF Classification System PowerPoint PPT Presentation
PIRSF Classification System - ... the button will show the PIRSF hierarchy in a DAG view with Pfam as the top node. 5. PIRSF hierarchy in DAG view (cont.) Pfam level. Hfam level. Subfam level ...
... the button will show the PIRSF hierarchy in a DAG view with Pfam as the top node. 5. PIRSF hierarchy in DAG view (cont.) Pfam level. Hfam level. Subfam level ...
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APAN e-Science Workshop e-Bio System for Bio-Knowledge Discovery PowerPoint PPT Presentation
APAN e-Science Workshop e-Bio System for Bio-Knowledge Discovery - New discoveries of biological knowledge are published in scientific journals ... motifs. Prosite, pfam, BLOCKS, InterPro. Keyword querying and motif detection ...
New discoveries of biological knowledge are published in scientific journals ... motifs. Prosite, pfam, BLOCKS, InterPro. Keyword querying and motif detection ...
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Sequence Analysis using Bioinformatics tools PowerPoint PPT Presentation
Sequence Analysis using Bioinformatics tools - Lycopersicon esculentum. GRAS Motif. Pfam tool. GAI, RGA, SCR ... Repressor of GA responses and involved in gibberellic acid mediated signaling. ...
Lycopersicon esculentum. GRAS Motif. Pfam tool. GAI, RGA, SCR ... Repressor of GA responses and involved in gibberellic acid mediated signaling. ...
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Evaluating genes and transcripts in Ensembl PowerPoint PPT Presentation
Evaluating genes and transcripts in Ensembl - refined EST matches using EST2GENOME, spangle. Pfam ... Orthology can provide useful confirmation. If no description, check for any Family description ...
refined EST matches using EST2GENOME, spangle. Pfam ... Orthology can provide useful confirmation. If no description, check for any Family description ...
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Tools for Protein Informatics PowerPoint PPT Presentation
Tools for Protein Informatics - Screening for membership in a family or superfamily. ... Pfam Prints SCOP. ProDom COG MSD. CD Search PDB. Blocks Systers. Homstrad Pandit ...
Screening for membership in a family or superfamily. ... Pfam Prints SCOP. ProDom COG MSD. CD Search PDB. Blocks Systers. Homstrad Pandit ...
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A statistical framework for genomic data fusion PowerPoint PPT Presentation
A statistical framework for genomic data fusion - Generate hydropathy profile from amino acid sequence using Kyte-Doolittle index. ... hydropathy profile. KFFT. Pfam HMM. protein sequence. KHMM. BLAST. protein ...
Generate hydropathy profile from amino acid sequence using Kyte-Doolittle index. ... hydropathy profile. KFFT. Pfam HMM. protein sequence. KHMM. BLAST. protein ...
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Hidden Markov Models (HMM) in Sequence Analysis PowerPoint PPT Presentation
Hidden Markov Models (HMM) in Sequence Analysis - PFAM:Protein families database of alignments and HMMs. HMMpro at www.netid.com,(Baldi, Chauvin and Mittal-Henkle) HMMER at hmmer.wustl. ... dry dryish damp soggy ...
PFAM:Protein families database of alignments and HMMs. HMMpro at www.netid.com,(Baldi, Chauvin and Mittal-Henkle) HMMER at hmmer.wustl. ... dry dryish damp soggy ...
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The Genome Access Course Protein Structure PowerPoint PPT Presentation
The Genome Access Course Protein Structure - To be sure - use ORF finder at NCBI. ORF finder to BLAST ... with other automated DBs (Pfam-B, DOMO), useful for seeing if region appears in ...
To be sure - use ORF finder at NCBI. ORF finder to BLAST ... with other automated DBs (Pfam-B, DOMO), useful for seeing if region appears in ...
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The Genome Access Course Protein Structure PowerPoint PPT Presentation
The Genome Access Course Protein Structure - High quality; nice graphics. Alignment of. Representative. Members. Description ... Pfam, SMART, ProDom, PRINTS, and Prosite domains. High quality annotation ...
High quality; nice graphics. Alignment of. Representative. Members. Description ... Pfam, SMART, ProDom, PRINTS, and Prosite domains. High quality annotation ...
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T-COFFEE, a novel method for Multiple Sequence Alignments PowerPoint PPT Presentation
T-COFFEE, a novel method for Multiple Sequence Alignments - T-COFFEE, a novel method for Multiple Sequence Alignments C dric Notredame WHO ? WHO USES T-Coffee ? Dali Domain Dictionnary Pfam SwissProt WHO Makes T-Coffee ?
T-COFFEE, a novel method for Multiple Sequence Alignments C dric Notredame WHO ? WHO USES T-Coffee ? Dali Domain Dictionnary Pfam SwissProt WHO Makes T-Coffee ?
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Remote Homology detection: A motif based approach PowerPoint PPT Presentation
Remote Homology detection: A motif based approach - A method based on presence of discrete sequence motifs for ... The Blocks database combines various databases such as pFAM, PRINTs, ProDom, DOMO and InterPro. ...
A method based on presence of discrete sequence motifs for ... The Blocks database combines various databases such as pFAM, PRINTs, ProDom, DOMO and InterPro. ...
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Evolving Models of Biological Sequence Similarity PowerPoint PPT Presentation
Evolving Models of Biological Sequence Similarity - a molecule composed of a linear sequence of smaller ... ( e.g. Pfam, SCOP) Organize around functional and homologous groups. ... Open opportunity, SCOP catalog ...
a molecule composed of a linear sequence of smaller ... ( e.g. Pfam, SCOP) Organize around functional and homologous groups. ... Open opportunity, SCOP catalog ...
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Introduction to biological databases 2 PowerPoint PPT Presentation
Introduction to biological databases 2 - PRINTS Aligned motifs. Pfam HMM (Hidden Markov Models) SMART HMM. TIGRfam HMM. DOMO Aligned motifs ... ATOM 2 CA ALA A 1 -37.691 14.156 98.995 1.00 72.12 C ...
PRINTS Aligned motifs. Pfam HMM (Hidden Markov Models) SMART HMM. TIGRfam HMM. DOMO Aligned motifs ... ATOM 2 CA ALA A 1 -37.691 14.156 98.995 1.00 72.12 C ...
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Standard Annotation PowerPoint PPT Presentation
Standard Annotation - Clear credit to where the annotation was done. Community Input by Wiki-style ... Classification: SCOP, CATH, pfam. Ligand: nature, structure; where, relevant? ...
Clear credit to where the annotation was done. Community Input by Wiki-style ... Classification: SCOP, CATH, pfam. Ligand: nature, structure; where, relevant? ...
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Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discove PowerPoint PPT Presentation
Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discove - To provide a global resource for the advancement of ... SCOP/CATH. BioCyc. Pfam. Reactome. Enzyme Classification. PubMed. GeneRIF. IHOP. Abstract search ...
To provide a global resource for the advancement of ... SCOP/CATH. BioCyc. Pfam. Reactome. Enzyme Classification. PubMed. GeneRIF. IHOP. Abstract search ...
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EARTH 3'1 SMP LAYOUT PowerPoint PPT Presentation
EARTH 3'1 SMP LAYOUT - Satisfying remote data and token request immediately ... N-Queen, Fibonacci, tomcatv, cannon, Ping-Pong, Paraffins, ATGC. New Benchmark: HMMER PFAM ...
Satisfying remote data and token request immediately ... N-Queen, Fibonacci, tomcatv, cannon, Ping-Pong, Paraffins, ATGC. New Benchmark: HMMER PFAM ...
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Protein Clustering to Assemble Families of Homeomorphic Proteins PowerPoint PPT Presentation
Protein Clustering to Assemble Families of Homeomorphic Proteins - Pfam-A - a collection of domain families created using profile HMMs built on ... Sn=Tp(Tp Fn) Specificity = the percentage of predicted linker residues that ...
Pfam-A - a collection of domain families created using profile HMMs built on ... Sn=Tp(Tp Fn) Specificity = the percentage of predicted linker residues that ...
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Using the Core Facility HansErik G' Aronson PowerPoint PPT Presentation
Using the Core Facility HansErik G' Aronson - Core Facility User Accounts. Short description of new projects for reporting purposes. ... DOE JGI Fugu (Pufferfish) assembly. WashU Pfam HMMs (GeneMatcher2 only) ...
Core Facility User Accounts. Short description of new projects for reporting purposes. ... DOE JGI Fugu (Pufferfish) assembly. WashU Pfam HMMs (GeneMatcher2 only) ...
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Protein World PowerPoint PPT Presentation
Protein World - At this moment more than 80 genomes have been sequenced and published, of all ... Domain-based clusterings: Prosite, Pfam, ProDom, Prints, Domo, Blocks ...
At this moment more than 80 genomes have been sequenced and published, of all ... Domain-based clusterings: Prosite, Pfam, ProDom, Prints, Domo, Blocks ...
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Rafael C Jimenez rafael@ebi.ac.uk PowerPoint PPT Presentation
Rafael C Jimenez rafael@ebi.ac.uk - Protein (domain, PTM, literature ... Sequence alignment data Summaries PowerPoint Presentation EMAP data Protein-protein interaction data PowerPoint ...
Protein (domain, PTM, literature ... Sequence alignment data Summaries PowerPoint Presentation EMAP data Protein-protein interaction data PowerPoint ...
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PROTEIN PATTERN DATABASES PowerPoint PPT Presentation
PROTEIN PATTERN DATABASES - protein pattern databases
protein pattern databases
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Identification of Protein Domains PowerPoint PPT Presentation
Identification of Protein Domains - Let's untrivialize by allowing for gaps: insertions and deletions. Start off with the PSSM HMM. ... insertions: Introduce new states Ij match insertions ...
Let's untrivialize by allowing for gaps: insertions and deletions. Start off with the PSSM HMM. ... insertions: Introduce new states Ij match insertions ...
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Orthology Analysis PowerPoint PPT Presentation
Orthology Analysis - Pairwise orthology confidence by orthostrapping' ... Orthology is not transitive! ... 286356 pairwise orthology assignments ( 75% orthostrap) ...
Pairwise orthology confidence by orthostrapping' ... Orthology is not transitive! ... 286356 pairwise orthology assignments ( 75% orthostrap) ...
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PROTEIN PATTERN DATABASES PowerPoint PPT Presentation
PROTEIN PATTERN DATABASES - ... models), can use two modes ls or fs, all domains should be matched with ls ... expressions, profiles, fingerprints, Hidden Markov Models and ProDom domains ...
... models), can use two modes ls or fs, all domains should be matched with ls ... expressions, profiles, fingerprints, Hidden Markov Models and ProDom domains ...
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The evolution of the immune system in chicken and higher vertebrates PowerPoint PPT Presentation
The evolution of the immune system in chicken and higher vertebrates - Chicken immunosystem project is part of WP1, 'Translational Medicine through ... Avian Cytokines Group, Institute for Animal Health, Compton (UK) (Prof. dr. Pete ...
Chicken immunosystem project is part of WP1, 'Translational Medicine through ... Avian Cytokines Group, Institute for Animal Health, Compton (UK) (Prof. dr. Pete ...
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BLOCKS PowerPoint PPT Presentation
BLOCKS - BLOCKS http://www.blocks.fhcrc.org/ Multiply aligned ungapped segments corresponding to most highly conserved regions of proteins- represented in profile
BLOCKS http://www.blocks.fhcrc.org/ Multiply aligned ungapped segments corresponding to most highly conserved regions of proteins- represented in profile
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My Favorite Pathway: Glycolysis/Gluconeogenesis PowerPoint PPT Presentation
My Favorite Pathway: Glycolysis/Gluconeogenesis - My Favorite Pathway: Glycolysis/Gluconeogenesis. Pallavi Penumetcha. 11/25/08. Glycolysis (RAST) ... Example of How to Investigate One Enzyme. Enzyme 3.1.3.11 ...
My Favorite Pathway: Glycolysis/Gluconeogenesis. Pallavi Penumetcha. 11/25/08. Glycolysis (RAST) ... Example of How to Investigate One Enzyme. Enzyme 3.1.3.11 ...
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Lab7 PowerPoint PPT Presentation
Lab7 - Arial Calibri Courier New Office Theme Lab7 Sean Eddy s Lab HMMER Introduction HMMER executables Installation Hmmbuild : build a ...
Arial Calibri Courier New Office Theme Lab7 Sean Eddy s Lab HMMER Introduction HMMER executables Installation Hmmbuild : build a ...
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S' pombe PowerPoint PPT Presentation
S' pombe - Functional annotation (Using GO, from literature curation, functional transfer ... Dubious 67. No GO S. pombe 567 11.5% (c.f. S. cerevisiae 612 10.5%) GO terms ...
Functional annotation (Using GO, from literature curation, functional transfer ... Dubious 67. No GO S. pombe 567 11.5% (c.f. S. cerevisiae 612 10.5%) GO terms ...
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NIGMS Protein Structure Initiative: Target Selection Workshop ADDA and remote homologue detection PowerPoint PPT Presentation
NIGMS Protein Structure Initiative: Target Selection Workshop ADDA and remote homologue detection - Liisa Holm. Institute of Biotechnology. University of Helsinki. Definitions ... Heger & Holm (2003) J Mol Biol 328, 749-767. Heger & al (2005) Nucl. Acids Res. ...
Liisa Holm. Institute of Biotechnology. University of Helsinki. Definitions ... Heger & Holm (2003) J Mol Biol 328, 749-767. Heger & al (2005) Nucl. Acids Res. ...
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Bioinformatics Resources and Tools on the Web: A Primer PowerPoint PPT Presentation
Bioinformatics Resources and Tools on the Web: A Primer - Much of this material comes from the Boston University course: BF527 ... Nematode: http://www.wormbase.org/ Nucleic Acids Research Database Issue ...
Much of this material comes from the Boston University course: BF527 ... Nematode: http://www.wormbase.org/ Nucleic Acids Research Database Issue ...
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Functional annotation PowerPoint PPT Presentation
Functional annotation - Functional annotation Datasources Konstantinos Mavrommatis Head of Omics group DOE-JGI Kmavrommatis@lbl.gov
Functional annotation Datasources Konstantinos Mavrommatis Head of Omics group DOE-JGI Kmavrommatis@lbl.gov
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Proteomics Data Interoperation with Applications to Integrated Datamining and Enhanced Information Retrieval PowerPoint PPT Presentation
Proteomics Data Interoperation with Applications to Integrated Datamining and Enhanced Information Retrieval - Proteomics Data Interoperation with Applications to Integrated Datamining and Enhanced Information Retrieval Andrew Smith Thesis Defense 8/25/2006
Proteomics Data Interoperation with Applications to Integrated Datamining and Enhanced Information Retrieval Andrew Smith Thesis Defense 8/25/2006
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Genome Annotation Continued PowerPoint PPT Presentation
Genome Annotation Continued - Genome Annotation Continued This week s lab. Genome annotation - web based databases for assigning gene function.
Genome Annotation Continued This week s lab. Genome annotation - web based databases for assigning gene function.
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Welcome to the Protein Database Tutorial PowerPoint PPT Presentation
Welcome to the Protein Database Tutorial - Images shown may not be up to date, so results on your searches may be different, ... Cultivar (stock) from which the gene was sequenced. ...
Images shown may not be up to date, so results on your searches may be different, ... Cultivar (stock) from which the gene was sequenced. ...
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Proteins Secondary Structure Predictions PowerPoint PPT Presentation
Proteins Secondary Structure Predictions - Structural Bioinformatics Proteins Secondary Structure Predictions
Structural Bioinformatics Proteins Secondary Structure Predictions
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Acknowledgements PowerPoint PPT Presentation
Acknowledgements - Comparative analysis of novel proteins from the CATH family of zinc peptidases Debanu Das1,2, Abhinav Kumar1,2, Lukasz Jaroszewski1,3 and Ashley Deacon1,2
Comparative analysis of novel proteins from the CATH family of zinc peptidases Debanu Das1,2, Abhinav Kumar1,2, Lukasz Jaroszewski1,3 and Ashley Deacon1,2
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Acknowledgements PowerPoint PPT Presentation
Acknowledgements - Comparative Analysis of Novel Proteins from the CATH Family of Zinc Peptidases Debanu Das1,2, Abhinav Kumar1,2, Lukasz Jaroszewski1,3 and Ashley Deacon1,2
Comparative Analysis of Novel Proteins from the CATH Family of Zinc Peptidases Debanu Das1,2, Abhinav Kumar1,2, Lukasz Jaroszewski1,3 and Ashley Deacon1,2
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??? ????? PowerPoint PPT Presentation
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Bio-Trac 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
Bio-Trac 25 (Proteomics: Principles and Methods) - Title: Protein Family Classification for Functional Genomics Author: wuc Last modified by: zh9 Created Date: 3/9/2001 10:06:29 PM Document presentation format
Title: Protein Family Classification for Functional Genomics Author: wuc Last modified by: zh9 Created Date: 3/9/2001 10:06:29 PM Document presentation format
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Extra credit problem PowerPoint PPT Presentation
Extra credit problem - Look at HMM alignment. Transmembrane Domains (TMHMM) http://www.cbs.dtu.dk/services/TMHMM ... Domains: Possibly a diverged tick' domain. Weak hit (below Noise ...
Look at HMM alignment. Transmembrane Domains (TMHMM) http://www.cbs.dtu.dk/services/TMHMM ... Domains: Possibly a diverged tick' domain. Weak hit (below Noise ...
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Bio-Trac 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
Bio-Trac 25 (Proteomics: Principles and Methods) - Molecular Biology Database Collection (http://nar.oupjournals.org/cgi/content ... WIT: Functional Curation and Metabolic Models. BRENDA: Enzyme Database ...
Molecular Biology Database Collection (http://nar.oupjournals.org/cgi/content ... WIT: Functional Curation and Metabolic Models. BRENDA: Enzyme Database ...
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Protein Bioinformatics Course PowerPoint PPT Presentation
Protein Bioinformatics Course - Protein Bioinformatics Course Matthew Betts & Rob Russell AG Russell (Protein Evolution) Course overview Day 1 - Modularity Day 2 - Interactions Day 3 - Modularity ...
Protein Bioinformatics Course Matthew Betts & Rob Russell AG Russell (Protein Evolution) Course overview Day 1 - Modularity Day 2 - Interactions Day 3 - Modularity ...
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Presentaci PowerPoint PPT Presentation
Presentaci - Alineamiento de secuencias. B squeda de hom logos. Alineamientos m ltiples. Patrones y perfiles. Curso de verano de Bioinform tica de la UCM
Alineamiento de secuencias. B squeda de hom logos. Alineamientos m ltiples. Patrones y perfiles. Curso de verano de Bioinform tica de la UCM
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MOSFET%20IV%20CHARACTERISTICS PowerPoint PPT Presentation
MOSFET%20IV%20CHARACTERISTICS - MOSFET IV CHARACTERISTICS Lot Number = F050118 Wafer Number = D4 Date = 11-13-2006 Process = SMFL CMOS Product = DAC03 NMOS L/W = 4/16
MOSFET IV CHARACTERISTICS Lot Number = F050118 Wafer Number = D4 Date = 11-13-2006 Process = SMFL CMOS Product = DAC03 NMOS L/W = 4/16
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PowerPoint PPT Presentation
- Title: PowerPoint Presentation Author: blatter Last modified by: marie-claude blatter Created Date: 1/3/2005 2:21:26 PM Document presentation format
Title: PowerPoint Presentation Author: blatter Last modified by: marie-claude blatter Created Date: 1/3/2005 2:21:26 PM Document presentation format
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Welcome to the Protein Database Tutorial PowerPoint PPT Presentation
Welcome to the Protein Database Tutorial - This tutorial will describe how to navigate the section of Gramene that provides ... Cultivar (stock) from which the gene was sequenced. ...
This tutorial will describe how to navigate the section of Gramene that provides ... Cultivar (stock) from which the gene was sequenced. ...
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pattern matching PowerPoint PPT Presentation
pattern matching - Functional genomics: finding out the function of all genes (and other parts) in a genome ... NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.3; R2=.02281121; TEXT='-LogE' ...
Functional genomics: finding out the function of all genes (and other parts) in a genome ... NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.3; R2=.02281121; TEXT='-LogE' ...
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IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES PowerPoint PPT Presentation
IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES - IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES L. Coin and R. Durbin Wellcome Trust Sanger Institute BIOINFORMATICS 2004 Presented by: Oscar Sanchez Plazas
IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES L. Coin and R. Durbin Wellcome Trust Sanger Institute BIOINFORMATICS 2004 Presented by: Oscar Sanchez Plazas
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