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What is MSA (Multiple Sequence Alignment)? What is it good for? How do I use it? Software and algorithms The programs How they work? Which to use? In practice Get the sequences Reformat them Evaluate the alignment Realign or modify the alignment Add or subtract sequence We have alredy discussed Lec 09
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Sunday, November 28, 7:49:01 PM Lec 09 Platform, software and algorithm selection Software's The best What’s available The easiest to use The best output Algorithm The most accurate The best for your problem What’s available What you are familiar with Web-basedCentral serverLocal computer Platforms
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Sunday, November 28, 7:49:01 PM Main applications of MSA Lec 09
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Sunday, November 28, 7:49:01 PM Get the sequences: databases GenBank: An annotated collection of all publicly available nucleotide and protein sequences. RefSeq: NCBI non-redundant set of reference sequences, including genomic DNA, transcript (RNA), and protein products. UniProt Consortium Database: Universal protein knowledgebase, a central resource of protein sequence and function from Swiss-Prot, TrEMBL and PIR. Entrez Gene: Gene-centered information at NCBI. UniGene: Unified clusters of ESTs and full-length mRNA sequences. OMIM: Online Mendelian inheritance in man: a catalog of human genetic and genomic disorders. Model Organism Genome Databases: MGD, RGD, SGD, Flybase… GeneCards: Integrated database of human genes, maps, proteins and diseases. SNP Consortium Database. Lec 09
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Sunday, November 28, 7:49:01 PM Get the sequences: Entrez Text Searches Lec 09 http://www.ncbi.nlm.nih.gov/sites/gquery
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Sunday, November 28, 7:49:01 PM Entrez Gene Lec 09 http://www.ncbi.nlm.nih.gov/gene
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Sunday, November 28, 7:49:01 PM UniProt Consortium Databases (http://www.uniprot.org)http://www.uniprot.org Lec 09 Number of explicitly cross-referenced databases: 126
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Sunday, November 28, 7:49:01 PM UniProt Text Search Lec 09 http://www.uniprot.org/
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Sunday, November 28, 7:49:01 PM UniProt Sequence Report Lec 09
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Sunday, November 28, 7:49:01 PM PIR Text Search Lec 09 http://pir.georgetown.edu/pirwww/search/textsearch.shtml
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Sunday, November 28, 7:49:01 PM OMIM: Online Mendelian Inheritance in Man Lec 09 http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim&TabCmd=Limits
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Sunday, November 28, 7:49:01 PM Protein Family Databases Whole Proteins PIRSF: A Network Classification System of Protein Families COG (Clusters of Orthologous Groups) of Complete Genomes ProtoNet: Automated Hierarchical Classification of Proteins Protein Domains Pfam: Alignments and HMM Models of Protein Domains SMART: Protein Domain Families CDD: Conserved Domain Database Protein Motifs PROSITE: Protein Patterns and Profiles BLOCKS: Protein Sequence Motifs and Alignments PRINTS: Protein Sequence Motifs and Signatures Integrated Family Databases iProClass: Superfamilies/Families, Domains, Motifs, Rich Links InterPro: Integrate Pfam, PRINTS, PROSITES, ProDom, SMART, PIRSF, SuperFamily Lec 09
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Sunday, November 28, 7:49:01 PM Lec 09 http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml PIRSF: A Network Classification System of Protein Families
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Sunday, November 28, 7:49:01 PM COG: Clusters of Orthologous Groups of proteins Lec 09 http://www.ncbi.nlm.nih.gov/COG/
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Sunday, November 28, 7:49:01 PM Domain Classification Lec 09 http://pir.georgetown.edu/pirwww/dbinfo/iproclass.shtml
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Sunday, November 28, 7:49:01 PM Lec 09 Domain Classification InterPro Gene3D
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Sunday, November 28, 7:49:01 PM Protein Motifs Lec 09
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Sunday, November 28, 7:49:01 PM Databases of Protein Functions Metabolic Pathways, Enzymes, and Compounds Enzyme Classification: Classification and Nomenclature of Enzyme-Catalysed Reactions (EC-IUBMB) KEGG (Kyoto Encyclopedia of Genes and Genomes): Metabolic Pathways LIGAND (at KEGG): Chemical Compounds, Reactions and Enzymes EcoCyc: Encyclopedia of E. coli Genes and Metabolism MetaCyc: Metabolic Encyclopedia (Metabolic Pathways) BRENDA: Enzyme Database UM-BBD: Microbial Biocatalytic Reactions and Biodegradation Pathways Cellular Regulation and Gene Networks EpoDB: Genes Expressed during Human Erythropoiesis BIND: Descriptions of interactions, molecular complexes and pathways DIP: Catalogs experimentally determined interactions between proteins BioCarta: Biological pathways of human and mouse GO: Gene Ontology Consortium Database Lec 09
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Sunday, November 28, 7:49:01 PM KEGG Metabolic & Regulatory Pathways KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks, the information of genes and proteins, and of chemical compounds and reactions. http://www.genome.jp/kegg/pathway.html http://www.genome.jp/kegg/pathway.html#metabolism Lec 09
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Sunday, November 28, 7:49:01 PM Multiple Genome Alignment MultiPipMaker - output MGA Michael Höhl, Stefan Kurtz,Enno Ohlebusch Efficient Multiple Genome Alignment Bioinformatics, Vol. 18 (S1): S312-S320, 2002 http://bibiserv.techfak.uni- bielefeld.de/mga/ref.html PipMaker and MultiPipMaker Schwartz S, Elnitski L, Li M, et al. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences NUCLEIC ACIDS RES 31 (13): 3518-3524 JUL 1 2003 http://bio.cse.psu.edu/pipmaker/ MAVID Bray N and Pachter L,MAVID multiple alignment server, Nucleic Acids Research 2003 31: 3525- 3526 http://baboon.math.berkeley.edu/mavid/ http://www-gsd.lbl.gov/vista/ Lec 09
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Sunday, November 28, 7:49:01 PM Multiple Genome Alignment Lec 09 Genomic Targets for Comparative Sequencing http://genome.ucsc.edu/
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