Molecular Biology Databases - PowerPoint Presentation

Slide1

Molecular Biology DatabasesSlide2

Tour of the major

molecular biology databases

A database is an

indexed

collection

of information

There is a tremendous amount of information about biomolecules in publicly available databases.

Today, we will just look at some of the main databases and what kind of information they contain.Slide3

Data about Databases

Nucleic Acids research publishes an annual database issue.

2009 issue

lists

1170 editorially

selected databases (link on course web site)

Small excerpt from the A's:

AARSDB:

Aminoacyl-tRNA

synthetase

sequences

ABCdb

: ABC transporters

AceDB

: C.

elegans

, S.

pombe

, and human sequences and genomic information

ACTIVITY: Functional DNA/RNA site activity

ALFRED: Allele frequencies and DNA polymorphismsSlide4

Located Sequence Features

Indexing relevant data isn’t always easy

Naming schemes are always in flux, vary across communities, and are often controversial.

Descriptions of phenotypes are very difficult to standardize (even many clinical ones)

Genome sequences provide a clear reference

A “located sequence feature” (place on a chromosome) is unambiguous and biologically meaningful

Closely related to the molecular concept of a gene.Slide5

What can be discovered about a gene by a database search?

Best to have specific

informational goals

:

Evolutionary information

: homologous genes, taxonomic distributions, allele frequencies, synteny, etc.

Genomic information

: chromosomal location, introns, UTRs, regulatory regions, shared domains, etc.

Structural information

: associated protein structures, fold types, structural domains

Expression information

: expression specific to particular tissues, developmental stages, phenotypes, diseases, etc.

Functional information

: enzymatic/molecular function, pathway/cellular role, localization, role in diseasesSlide6

Using a database

How to get information out of a database:

Summaries

: how many entries, average or extreme values; rates of change, most recent entries, etc.

Browsing

: getting a sense of the kind and quality of information available, e.g. checking familiar records

Search

: looking for specific, predefined information

“Key” to searching a database:

Must identify the element(s) of the database that are of interest somehow:

Gene name, symbol, location or other identifying information.

Sequences of genes, mRNAs, proteins, etc.

A crossreference from another database or database generated id.Slide7

Searching for information

about genes and their products

Gene and gene product databases are often organized by sequence

Genomic sequence encodes all traits of an organism.

Gene products are uniquely described by their sequences.

Similar sequences among biomolecules indicates both similar function and an evolutionary relationship

Macromolecular sequences provide biologically meaningful keys for searching databasesSlide8

Searching sequence databases

Starting from a sequence alone, find information about it

Many kinds & sources of input sequences

Genomic, expressed, protein (amino acid vs. nucleic acid)

Complete or fragmentary sequences

Goal is to retrieve a set of similar sequences.

Exact matches are rare, and not always interesting

Both small differences (mutations) and large (not required for function) within “similar” sequences can be biologically important.Slide9

What might we want

to know about a sequence?

Is this sequence similar to any known genes? How close is the best match? Significance?

What do we know about that gene?

Genomic (chromosomal location, allelic information, regulatory regions, etc.)

Structural (known structure? structural domains? etc.)

Functional (molecular, cellular & disease)

Evolutionary information:

Is this gene found in other organisms?

What is its taxonomic tree?Slide10

NCBI and Entrez

One of the most useful and comprehensive database collections is the NCBI, part of the National Library of Medicine.

Home to GenBank, PubMed & many other familiar DBs.

NCBI provides interesting summaries, browsers, and search tools

Entrez is their database search interface

http://www.ncbi.nlm.nih.gov/Entrez

Can search on gene names, chromosomal location, diseases, articles, keywords...Slide11
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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 likely homologous).

Can start with nucleotide or amino acid sequence, and search for either (or both)

Many options

E.g. ignore low information (repetitive) sequence, set significance critical value

Defaults are not always appropriate

: READ THE NCBI EDUCATION PAGES!Slide13

Main BLAST pageSlide14

A demonstration sequence

atgcacttgagcagggaagaaatccacaaggactcaccagtctcctggtctgcagagaagacagaatcaacatgagcacagcaggaaaagtaatcaaatgcaaagcagctgtgctatgggagttaaagaaacccttttccattgaggaggtggaggttgcacctcctaaggcccatgaagttcgtattaagatggtggctgtaggaatctgtggcacagatgaccacgtggttagtggtaccatggtgaccccacttcctgtgattttaggccatgaggcagccggcatcgtggagagtgttggagaaggggtgactacagtcaaaccaggtgataaagtcatcccactcgctattcctcagtgtggaaaatgcagaatttgtaaaaacccggagagcaactactgcttgaaaaacgatgtaagcaatcctcaggggaccctgcaggatggcaccagcaggttcacctgcaggaggaagcccatccaccacttccttggcatcagcaccttctcacagtacacagtggtggatgaaaatgcagtagccaaaattgatgcagcctcgcctctagagaaagtctgtctcattggctgtggattttcaactggttatgggtctgcagtcaatgttgccaaggtcaccccaggctctacctgtgctgtgtttggcctgggaggggtcggcctatctgctattatgggctgtaaagcagctggggcagccagaatcattgcggtggacatcaacaaggacaaatttgcaaaggccaaagagttgggtgccactgaatgcatcaaccctcaagactacaagaaacccatccaggaggtgctaaaggaaatgactgatggaggtgtggatttttcatttgaagtcatcggtcggcttgacaccatgatggcttccctgttatgttgtcatgaggcatgtggcacaagtgtcatcgtaggggtacctcctgattcccaaaacctctcaatgaaccctatgctgctactgactggacgtacctggaagggagctattcttggtggctttaaaagtaaagaatgtgtcccaaaacttgtggctgattttatggctaagaagttttcattggatgcattaataacccatgttttaccttttgaaaaaataaatgaaggatttgacctgcttcactctgggaaaagtatccgtaccattctgatgttttgagacaatacagatgttttcccttgtggcagtcttcagcctcctctaccctacatgatctggagcaacagctgggaaatatcattaattctgctcatcacagattttatcaataaattacatttgggggctttccaaagaaatggaaattgatgtaaaattatttttcaagcaaatgtttaaaatccaaatgagaactaaataaagtgttgaacatcagctggggaattgaagccaataaaccttccttcttaaccattSlide15

Major choices:

Translation

Database

Filters

Restrictions

MatrixSlide16

Formatted blast outputSlide17

Close hit:

Macaque ADH

alphaSlide18

Distant hit:

L-

threonine

3-dehydrogenase from a

thermophilic

bacteriumSlide19

ParametersSlide20

Click on:Slide21

…Slide22

Taxonomy report

(link from “Results of BLAST” page)Slide23

What did we just do?

Identify loci (genes) associated with the sequence.

Input was

human Alcohol

Dehydrogenase

1A

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.

But there’s

much more

that can be found on these genes, even just inside NCBI…Slide24

Blink:

Precomputed

blastSlide25

Conserved domainsSlide26

NCBI version of KEGG &

EcoCycSlide27
Slide28

More from Entrez GeneSlide29

And more…Slide30
Slide31

PubMedSlide32
Slide33

Gene Expression Slide34

Detailed expression informationSlide35

Genome map viewSlide36

OMIMSlide37
Slide38
Slide39

NCBI is not all there is...

Links to non-NCBI databases (see also “Link Out”)

Reactome for pathways (also KEGG)

HGNC for nomenclature

HPRD protein information

Regulatory / binding site DBs (e.g. CREB; some not linked)

IHOP (information hyperlinked over proteins)

Other important gene/protein resources not linked:

UniProt (most carefully annotated)

PDB (main macromolecular structure repository)

UCSC (best genome viewer & many useful ‘tracks’)

DIP / MINT (protein-protein interactions)

More: InterPro, MetaCyc, Enzyme, etc. etc.Slide40
Slide41
Slide42

Gene Names (not easy!)Slide43

Protein reference dbSlide44
Slide45
Slide46

…

…Slide47
Slide48

Take home messages

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)

These databases are moderately well cross-linked, and there are “linker” databases

Sequence is a good identifier, maybe even better than gene name!Slide49

Homework

Pick a favorite gene (or, if you don’t know any, how about looking up one of my favorites, PPAR-Delta) and gather information about it from at least five distinct resources

.

Readings

:

Nucleic Acids Research

online

Molecular Biology Database Collection in

2009

Nucl

. Acids Res.

2009 37: D1-

D4

doi

:10.1093/nar/gkn942

also, browse some of the entries themselves.

NCBI tutorial,

Entrez: Making use of its power.