Genomerelated databases

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Genome-related databases

• Helen Hed
• Umeå universitetsbibliotek

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What is bioinformatics?

• Synthesis of biology, computer science and
  information technology
• Goal generate new biological knowledge
• Develop algorithms, methods for analysis and
  interpretation, tools for supply and managment
• Computer-supplied management for analysis of
  DNA-, RNA- and protein sequencies.

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Can a librarian teach you bioinformatics?

• NO
• But she can show you
• What is available and
• How the databases are connected and
• Where to start

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Genome related databases

• Huge amounts of cell and molecular biology data
  is stored in hundreds of databases.
• Some tools make it easier to search and analyze
  the data.

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Presentation

• What do I work with?
• What do I already know in this field?
• What are my expectations during this class?
• What do you already know?
• What are your expectations?

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Genome-related databases and resources

• Sequence databases and related resources
• Genbank and RefSeq
• Nucleotide
• Protein
• Genome
• Structure
• OMIM
• Map Viewer

• Portals and other resources
• Entrez
• (Locus link)
• Entrez Gene
• Genes and diseases
• Blast
• Ensembl
• And more

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Entrez portal

• Portal to all NCBI genome related resources
  including PubMed

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Genbank

• Database of nucleotide sequences from 130 000
  organisms
• Gathered from DDBJ (DNA Data Bank of Japan), EMBL
  (European Molecular Biology Laboratory), and NCBI
  (National Center for Biotechnology Information).
• Updated daily
• Example of a sequence document

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Nucleotide

• Contains data about nucleotide sequences (both
  DNA and RNA) from different databases. The
  biggest is Genbank.
• In every sequence document there are references
  to the article where the sequence was first
  presented.
• Genetic code scheme. Translation from DNA
  molecule to amino acid.
• Amino acid abbreviations.

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Protein

• Contains protein sequence data collected from
  different databases.
• In every sequence document there is a reference
  to the article where the discovery of the
  sequence was decribed.

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RefSeq accession numbers

• Curated sequences
• NT_123456 (constructed genomic contigs)NM_123456
  (curated mRNAs)NC_123456 (curated
  proteins)NG_123456 (curated chromosomes)XP_12345
  6 (curated genomic regions)XM_123456
• With different statusPredicted, provisional,
  reviewd, validated, et c. http//www.ncbi.nlm.nih.
  gov/RefSeq/key.html

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Structure

• Contains visalization possibilities for
  3D-representation of structures
• For viewing the structures you need a plug-in
  that can be downloaded for free (Cn3D)

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Genome

• Contains data on the nucleotide sequences that
  constitutes a whole genome.
• There are both whole chromosomes and pieces of
  chromosomes from about 800 different organisms
• Gives a graphical overview of genomes and
  chromosomes (called sequence maps).

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OMIM Online Mendelian Inheritance in Man

• A database of human genes, genetic diceases and
  phenotypes
• Links to nucleotide, protein, structure and
  genome.

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Map viewer organism map

• Search for organism and find the right chromosome

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Locus Link

• A kind of portal for all molecular biology
  databases. Especially meant for finding
  information on a certain gene.
• Search on Google ncbi locuslink
• Will be replaced by Entrez Gene on March 1, 2005

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Entrez Gene

• A good starting point if you know what gene you
  want information about
• You can query on names, symbols, accessions,
  publications, GO terms, chromosome numbers, E.C.
  numbers, and many other attributes associated
  with genes and the products they encode.
• http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
  ene

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Genes and Disease

• Information about different genetic diseases an
  e-book
• Available from NCBIs Bookshelf
• Find the book in the booklist
• Search for the disease you need information about

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Practice excersises

• How many chromosomes does Anopheles gambiae have?
• Search for curated sequences (RefSeq) on actin
  mRNA for a mouse.
• Find a 3D picture of a stress protein.
• Search for documents on human albumin and find
  the information about who submitted the
  information.
• I dont know anything about porfyria but would
  like to know what it is. Is it heritable? And if
  so, on what chromosome is the gene for porphyria
  situated?

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Relationship between Entrez databases
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Blast

• A tool for comparing sequences
• Available at http//www.ncbi.nlm.nih.gov/BLAST/

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Other ways of accessing data

• DDBJ (DNA Data Bank of Japan),
• EMBL (European Molecular Biology Laboratory)
  Ensembl, and
• NCBI (National Center for Biotechnology
  Information).
• These three are the largest
• They exchange data daily
• Most data end up in these

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Searching the Internet
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Web resources

• Google is not the answer, its a tool
• Google Scholar is also not the answer, its a
  new Google-tool with less junk
• Scirus specialized search engine
• OAIster searches digital archioves (mostely
  free material)
• Citebase free alternative to ISI science
  citation index

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Helpful tools

• Google definegene
• Brainboost When did Frank Zappa die and why?
• Teoma resources
• Example search for genetics