1. Biological Databases Notes adapted from lecture notes of Dr. Larry Hunter at the University of Colorado

2. Tour of Major Biological Databases There is a tremendous amount of information about biomolecules in publicly available databases. There is a tremendous amount of information about biomolecules in publicly available databases. Today, we will look at a few of the main databases and what kind of information they contain. Today, we will look at a few of the main databases and what kind of information they contain. Lab project will give you a little practice at browsing databases Lab project will give you a little practice at browsing databases

3. What can be discovered about a gene by a database search? A little or a lot, depending on the gene A little or a lot, depending on the gene Evolutionary information: homologous genes, taxonomic distributions, allele frequencies, synteny, etc. Evolutionary information: homologous genes, taxonomic distributions, allele frequencies, synteny, etc. Genomic information: chromosomal location, introns, UTRs, regulatory regions, shared domains, etc. Genomic information: chromosomal location, introns, UTRs, regulatory regions, shared domains, etc. Structural information: associated protein structures, fold types, structural domains Structural information: associated protein structures, fold types, structural domains Expression information: expression specific to particular tissues, developmental stages, phenotypes, diseases, etc. Expression information: expression specific to particular tissues, developmental stages, phenotypes, diseases, etc. Functional information: enzymatic/molecular function, pathway/cellular role, localization, role in diseases Functional information: enzymatic/molecular function, pathway/cellular role, localization, role in diseases

4. Using a database How to get information out of a database: How to get information out of a database: Browsing: no targeted information to retrieve Browsing: no targeted information to retrieve Search: looking for particular information Search: looking for particular information Searching a database: Searching a database: Must have a key that identifies the element(s) of the database that are of interest. Must have a key that identifies the element(s) of the database that are of interest. Name of gene Name of gene Sequence of gene Sequence of gene Other information Other information Helps to have particular informational goals Helps to have particular informational goals

5. Searching for information about genes and their products Gene and gene product databases are often organized by sequence Gene and gene product databases are often organized by sequence Genomic sequence encodes all traits of an organism. Genomic sequence encodes all traits of an organism. Gene products are uniquely described by their sequences. Gene products are uniquely described by their sequences. Similar sequences among biomolecules indicates both similar function and an evolutionary relationship Similar sequences among biomolecules indicates both similar function and an evolutionary relationship Macromolecular sequences provide biologically meaningful keys for searching databases Macromolecular sequences provide biologically meaningful keys for searching databases

6. Searching sequence databases Start from sequence, find information about it Start from sequence, find information about it Many kinds of input sequences Many kinds of input sequences Could be amino acid or nucleotide sequence Could be amino acid or nucleotide sequence Genomic or mRNA/cDNA or protein sequence Genomic or mRNA/cDNA or protein sequence Complete or fragmentary sequences Complete or fragmentary sequences Exact matches are rare (even uninteresting in many cases), so often goal is to retrieve a set of similar sequences. Exact matches are rare (even uninteresting in many cases), so often goal is to retrieve a set of similar sequences. Both small (mutations) and large (required for function) differences within “similar” can be interesting. Both small (mutations) and large (required for function) differences within “similar” can be interesting.

7. What might we want to know about a sequence? Is this sequence similar to any known genes? How close is the best match? Significance? Is this sequence similar to any known genes? How close is the best match? Significance? What do we know about that gene? What do we know about that gene? Genomic (chromosomal location, allelic information, regulatory regions, etc.) Genomic (chromosomal location, allelic information, regulatory regions, etc.) Structural (known structure? structural domains? etc.) Structural (known structure? structural domains? etc.) Functional (molecular, cellular & disease) Functional (molecular, cellular & disease) Evolutionary information: Evolutionary information: Is this gene found in other organisms? Is this gene found in other organisms? What is its taxonomic tree? What is its taxonomic tree?

8. NCBI and Entrez

9. One of the most useful and comprehensive sources of databases is the NCBI, part of the National Library of Medicine. One of the most useful and comprehensive sources of databases is the NCBI, part of the National Library of Medicine. NCBI provides interesting summaries, browsers for genome data, and search tools NCBI provides interesting summaries, browsers for genome data, and search tools Entrez is their database search interface http://www.ncbi.nlm.nih.gov/Entrez Entrez is their database search interface http://www.ncbi.nlm.nih.gov/Entrez http://www.ncbi.nlm.nih.gov/Entrez Can search on gene names, sequences, chromosomal location, diseases, keywords,... Can search on gene names, sequences, chromosomal location, diseases, keywords,...

11. BLAST: Searching with a sequence Goals is to find other sequences that are more similar to the query than would be expected by chance (and therefore are homologous). Goals is to find other sequences that are more similar to the query than would be expected by chance (and therefore are homologous). Can start with nucleotide or amino acid sequence, and search for either (or both) Can start with nucleotide or amino acid sequence, and search for either (or both) Many options Many options E.g. ignore low information (repetitive) sequence, set significance critical value E.g. ignore low information (repetitive) sequence, set significance critical value Defaults are not always appropriate: READ THE NCBI EDUCATION PAGES! Defaults are not always appropriate: READ THE NCBI EDUCATION PAGES!

13. Major choices: Major choices: Translation Translation Database Database Filters Filters Restrictions Restrictions Matrix Matrix

16. Close hit: Rat ADH alpha

17. Distant hit: Human sorbitol dehydrogenase

18. Parameters (at bottom!)

19. Click on:

21. Taxonomy report (link from “Results of BLAST” page)

22. What did we just do? Identify loci (genes) associated with the sequence. Input was Alcohol Dehydrogenase Identify loci (genes) associated with the sequence. Input was Alcohol Dehydrogenase For each particular “hit”, we can look at that sequence and its alignment in more detail. For each particular “hit”, we can look at that sequence and its alignment in more detail. See similar sequences, and the organisms in which they are found. See similar sequences, and the organisms in which they are found. But there’s much more that can be found on these genes, even just inside NCBI… But there’s much more that can be found on these genes, even just inside NCBI…

26. More from Entrez Gene

27. And more…

28. PubMed

30. Gene Expression

31. Detailed expression information

35. NCBI is not all there is... Links to non-NCBI databases Links to non-NCBI databases Reactome & KEGG for pathways Reactome & KEGG for pathways HGNC for nomenclature HGNC for nomenclature UCSC Human Genome Browser UCSC Human Genome Browser Other important gene/protein resources not linked to: Other important gene/protein resources not linked to: UniProt (most carefully annotated) UniProt (most carefully annotated) PDB (main macromolecular structure repository) PDB (main macromolecular structure repository) Other key biological data sources Other key biological data sources Gene Ontology/Open Biological Ontologies Gene Ontology/Open Biological Ontologies Enzyme Enzyme Scientific society: iscb.org Scientific society: iscb.org Journals, Conferences… Journals, Conferences…

38. Gene Names: Harder than you think…

42. Take home messages There are a lot of molecular biology databases, containing a lot of valuable information There are a lot of molecular biology databases, containing a lot of valuable information Not even the best databases have everything (or the best of everything) Not even the best databases have everything (or the best of everything) These databases are moderately well cross- linked, and there are “linker” databases These databases are moderately well cross- linked, and there are “linker” databases Sequence is a good identifier, maybe even better than gene name! Sequence is a good identifier, maybe even better than gene name!