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Biology 4900. Biocomputing. Chapter 2. Molecular Databases and Data Analysis. Literature Databases. Online databases available at CSU Galileo JSTOR Online databases at other sites

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Biology 4900

Biology 4900

Biocomputing


Chapter 2

Chapter 2

Molecular Databases and Data Analysis


Literature databases
Literature Databases

  • Online databases available at CSU

    • Galileo

    • JSTOR

  • Online databases at other sites

    • PubMed. If you find a useful article, you can check PubMed Central to see if it is available online for free.

  • Where to get articles

    • PubMed Central

    • GIL

    • Interlibrary loan


Sources of molecular data
Sources of Molecular Data

DNA

RNA

protein

phenotype

protein

sequence

databases

cDNA

*ESTs

UniGene

genomic

DNA

databases

*Expressed Sequence Tags


Molecular databases
Molecular Databases

  • Primary Database

    • Archival - sequences submitted directly from experimental sequencing results

      • Very little interpretation

      • Anyone can submit; accuracy not checked

      • Examples

        • Nucleic Acid: EMBL, DDJB, GenBANK

        • Protein: Swiss-Prot, PIR, PDB

  • Secondary Databases

    • Curated– sequences are validated/checked and may be annotated

      • Refseq (nucleic acids and proteins, but limited to certain organisms)

      • TrEMBL, GenPept, Uniprot


Nucleic acid databases
Nucleic Acid Databases

  • Contain:

    • Nucleic acid sequences

      • Chain termination method (Sanger sequencing)

        • Used for sequences 100-1000 bp

      • Whole Genome Shotgun (WGS) Sequencing

        • Used for sequences >1000 bp

        • DNA chopped into little chunks

        • Sequenced using chain termination method (reads)

        • Numerous, overlapping reads are collected and assembled into sequence (computational methods)

    • Annotations for each sequence

      • Putative identification of open reading frames (ORFs = parts of gene that encode protein) in sequence

      • Putative intron(excised)/exon(retained) locations

      • Authors, dates, publication, etc.


International Nucleotide Sequence Database Collaboration(Public nucleotide and protein sequence databases)

Name: GenBank

Location: National Institutes of Health, National Center for Biotechnology Information

GenBank

Daily Info sharing

Daily Info sharing

DDBJ

EMBL

Daily Info sharing

Name: European Molecular Biology Laboratory (EMBL)

Location: European Bioinformatics Institute (EBI)

Name: DNA Database of Japan (DDBJ)

Location: National Institute of Genetics, Mishima


Genbank
GenBank

  • As of April 2011, There were approximately 126,551,501,141 bases in 135,440,924 sequence records in the traditional GenBank divisions.

  • Read the following paper: http://www.ncbi.nlm.nih.gov/pubmed/21071399

  • Home Page: http://www.ncbi.nlm.nih.gov/genbank/

Homo sapiens 14.9 billion bases

Mus musculus8.9b

Rattus norvegicus6.5b

Bos taurus 5.4b

Zea mays 5.0b

Sus scrofa 4.8b

Danio rerio3.1b

Strongylocentrotus purpurata 1.4b

Oryza sativa (japonica)1.2b

Nicotiana tabacum 1.2b

Most sequenced organisms


Genbank home page
GenBank Home Page


Ncbi resources
NCBI Resources

  • PubMed

  • BLAST

  • OMIM

  • Taxonomy Browser

  • Structure


Ncbi key features pubmed
NCBI key features: PubMed

  • National Library of Medicine's search service

  • 21 million citations from MEDLINE & others (as of 2011)

  • Links to other online journals

  • http://www.ncbi.nlm.nih.gov/pubmed

  • Starting point for most research




A “how to” pull-down menu links to tutorials Medical Subject Headings (MeSH)



PubMed search strategies language, etc.

Try the tutorial

Use boolean queries (capitalize AND, OR, NOT)

lipocalin AND disease

Try using limits (see Advanced search)

There are links to find Entrez entries and external resources


1 AND 2 language, etc.

1

2

lipocalin AND disease

(504 results)

1 OR 2

1

2

lipocalin OR disease

(2,500,000 results)

1 NOT 2

1

2

lipocalin NOT disease

(2,370 results)



Pubmed author search
PubMed Author Search language, etc.


Scholar google search
Scholar Google Search language, etc.

  • http://scholar.google.com/

  • Includes references that may not be found in PubMed


NCBI key features language, etc.

  • A search from NCBI main page will search:

  • the scientific literature;

  • DNA and protein sequence databases;

  • 3D protein structure data;

  • population study data sets;

  • assemblies of complete genomes

  • String search

    • Search by author, date, keyword, publication, etc.

Classroom exercise:

Author searches

Paper searches

Protein searches


Ncbi key features blast
NCBI key features: BLAST language, etc.

  • BLAST is…

  • Basic Local Alignment Search Tool

  • NCBI's sequence similarity search tool

  • supports analysis of DNA and protein databases

3CLN


NCBI key features: OMIM language, etc.

  • Online Mendelian Inheritance in Man

  • Catalog of human genes and genetic disorders


NCBI key features: Taxonomy Browser language, etc.

  • Browser for the major divisions of living organisms

  • (archaea, bacteria, eukaryota, viruses)

  • Taxonomy information such as genetic codes

  • Molecular data on extinct organisms

  • Useful to find a protein or gene from a species


NCBI key features: Structure language, etc.

  • Molecular Modelling Database (MMDB)

  • biopolymer structures obtained from

  • the Protein Data Bank (PDB)

  • Cn3D (a 3D-structure viewer)

  • vector alignment search tool (VAST)


Cn3D language, etc.

  • A 3D-structure viewer

  • Must download (ftp://ftp.ncbi.nlm.nih.gov/cn3d/Cn3D-4.3.msi)

  • Use to align structures identified as similar by VAST


Example researching beta globin
Example: Researching beta globin language, etc.

  • Beta globin is protein, so it will be found in 3 different types of databases

DNA

*RNA

Proteins

Entrez Protein

UniProt

PDB

SCOP

CATH

GenBank dbGSS

GenBank dbHTGS

GenBank dbSTS

GenBank Entrez Gene

GenBank dbEST

UniGene

Gene Expression Omnibus

*Because RNA is unstable, it can be transcribed into complementary DNA (cDNA)


Necessary yet annoying definitions
Necessary (yet annoying) Definitions language, etc.

  • Sequence Tagged Site (STS): Small DNA fragments with both DNA sequence data and mapping data (genes assigned to chromosomes)

  • Expressed Sequence Tags (EST): Partial DNA sequence of a complementary (cDNA) clone

    • Typically these are randomly-selected cDNA clones sequenced on a single strand (300-800 bp)

    • Useful for identifying novel genes

    • Higher rate of error

http://genome.wellcome.ac.uk/doc_WTD020755.html


Unigene
Unigene language, etc.

  • Unique Gene (Unigene) Project to create gene-oriented clusters by partitioning ESTs into non-redundant sets

    • http://www.ncbi.nlm.nih.gov/unigene

    • Ultimately there should be only 1 cluster per gene

    • Usually more than 1 due to errors

    • Types of errors

      • 2 or more clusters may represent different parts of the same gene

      • Sequence errors

      • Cloning artifacts (DNA transcribed during creation of cDNA that doesn’t correspond to authentic transcript)

EST’s

Unigene Cluster


Unigene1
Unigene language, etc.

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


Genbank flatfile
GenBank language, etc.Flatfile

  • A format for organizing genomic sequence data. Includes the following:

  • Sequence and annotations

  • Header

    • Locus name or accession number: unique to sequence description

    • Size: number of nucleotide bases or amino acid residues

    • Molecule: DNA, RNA, strandedness (ds, ss), and type of RNA or DNA

    • Genbank division code: 18 divisions (PRI = primate, PLN = plant, BAC = bacterial, etc.)

    • Date of last modification

  • Definition Line: brief description of sequence (e.g. source organism, protein/gene name, function)

  • Accession: unique identifier for a record

  • Version

    • May be more than one accession

    • Record modification (accession.1; accession.2)

    • GI: is specific to version; may be more than one

  • Keywords

  • Source: organism or clone description

  • Reference: publications that discuss data reported

  • Authors and Journal publication info

  • PubMed identifier: link to sequence record (abstract)

  • Features: vary (chromosomal info., coding info, protein id, % of each nucleotide)

  • Sequence Data

Jump to example


What is an accession number? language, etc.

An accession number is label that is used to identify a sequence. It is a (unique) string of letters and/or numbers that corresponds to a molecular sequence.

Examples (all for retinol-binding protein, RBP4):

X02775 GenBank genomic DNA sequence

NT_030059 Genomic contig (overlapping DNA fragments)

Rs7079946 dbSNP (single nucleotide polymorphism)

N91759.1 An expressed sequence tag (1 of 170)

NM_006744 RefSeq DNA sequence (from a transcript)

NP_007635 RefSeq protein

AAC02945 GenBank protein

Q28369 SwissProt protein

1KT7 Protein Data Bank structure record

DNA

RNA

protein


NCBI’s important language, etc.RefSeq project: best representative sequences

RefSeq (accessible via the main page of NCBI)

provides an expertly curated accession number that

corresponds to the most stable, agreed-upon “reference”

version of a sequence.

RefSeq identifiers include the following formats:

Complete genome NC_######

Complete chromosome NC_######

Genomic contig NT_######

mRNA (DNA format) NM_###### e.g. NM_006744

Protein NP_###### e.g. NP_006735


Unigene name search oncomodulin
UniGene language, etc. Name Search: Oncomodulin

All results listed

Allows filtering


Unigene name search select human oncomodulin
UniGene language, etc. Name Search: Select Human Oncomodulin

  • 4 Expressed Sequence Tags from 1 complementary DNA library

  • Identifies chromosome and map position on chromosome

  • Compares cluster transcripts with refseq proteins


Unigene name search select human oncomodulin1
UniGene language, etc. Name Search: Select Human Oncomodulin

Click on link for menu of other links:

Conserved domains

Gene summary

Protein sequence

Clicking on Protein sequence link then takes you to predicted protein sequence file (NP_006179.2) 


Unigene name search select human oncomodulin2
UniGene language, etc. Name Search: Select Human Oncomodulin

1

2

3

4

Once here, you can:

Open FASTA file

Run BLAST

Identify and view conserved domains

See related proteins


Access to sequences: Gene at NCBI language, etc.

Gene is a great starting point: it collects

key information on each gene/protein from

major databases. It covers all major organisms.

Example: RefSeq provides a curated, optimal accession number for each DNA (NM_000518 for beta globin DNA corresponding to mRNA) or protein (NP_000509)

These references should be more reliable data


Gene name search oncomodulin
Gene Name Search: language, etc.Oncomodulin

Returns list of gene entries for oncomodulin for different organisms

Click on a highlighted link to see details


Gene name search select human oncomodulin
Gene Name Search: Select Human language, etc.Oncomodulin

Summary of all gene information, including mapping (when available). Note that this sequence has been validated as a RefSeq.

Scrolling down, you can find link to protein data through UniProt. 


Gene name search link to oncomodulin protein
Gene Name Search: Link to language, etc.Oncomodulin Protein


Protein name search oncomodulin
Protein Name Search: language, etc.Oncomodulin

Notice that I filtered this search so that results show only human oncomodulin



FASTA format: language, etc.

versatile, compact with one header line

followed by a string of nucleotides or amino acids

in the single letter code


Comparison of Gene to other resources language, etc.

Gene: collects key information on each gene/protein from major databases. It covers all major organisms.

UniGene: Database with information on where in a body, when in development, and how abundantly a transcript is expressed

HomoloGene: Gathers information on sets of related proteins based on common genetic ancestry.


Homologene name search oncomodulin
Homologene language, etc. Name Search: Oncomodulin

Provides list of homologous (related) genes


Homologene name search oncomodulin1
Homologene language, etc. Name Search: Oncomodulin

Shows conserved domains of protein sequences. If you click on graphic, takes you to summary of domain/family information.


Expasy to access protein and dna sequences
ExPASy language, etc. to access protein and DNA sequences

  • ExPASy (Expert Protein Analysis System) sequence retrieval system

  • Visit http://www.expasy.ch/

  • Similar to Entrez for NCBI

Example: Search for calmodulin

Jump to Prosite


UniProt: language, etc.

a centralized protein database (uniprot.org)

This is separate from NCBI, and interlinked.


Uniprot calmodulin
UniProt language, etc.: Calmodulin

  • Search Results for bovine calmodulin (P62157)


Protein secondary structure pdbsum embl ebi
Protein Secondary Structure: language, etc.PDBSum (EMBL-EBI)

  • http://www.ebi.ac.uk/pdbsum/

  • Either enter PDB file or can load new/existing sequence



Genome Browsers language, etc.

Genomic DNA is organized in chromosomes. Genome browsers display ideograms (pictures) of chromosomes, with user-selected “annotation tracks” that display many kinds of information.

The two most essential human genome browsers are at Ensembl and UCSC. We will focus on UCSC (but the two are equally important). The browser at NCBI is not commonly used.


Ensembl genome browser (www.ensembl.org) language, etc.

click

human


enter language, etc.

beta globin


Ensembl output for language, etc.

beta globin includes views of chromosome 11 (top), the region (middle), and a detailed view (bottom).

There are various horizontal annotation tracks.


The UCSC Genome Browser language, etc.

  • This browser’s focus is on humans and other eukaryotes

  • you can select which tracks to display (and how much information for each track)

  • tracks are based on data generated by the UCSC team and by the broad research community

  • you can create “custom tracks” of your own data! Just format a spreadsheet properly and upload it

  • The Table Browser is equally important as the more visual Genome Browser, and you can move between the two


[1] Visit http://genome.ucsc.edu/, click Genome Browser language, etc.

[2] Choose organisms, enter query (beta globin), hit submit


[4] On the UCSC Genome Browser: language, etc.

--choose which tracks to display


Protein databases
Protein Databases language, etc.

  • What do they contain?

    • Amino acid sequences

      • Primary sequence

        • Direct submissions - protein sequencing

        • SWISS-PROT, PIR

      • Secondary sequence

        • Translations - putative proteins resulting from modifying (i.e. intron splicing) nucleic acid sequence

        • GenPept, TrEMBL

      • Structure

        • Protein Data Bank

    • Annotations

      • Function, domains, etc.


Swiss prot
SWISS-PROT language, etc.

  • Created by Amos Bairoch in 1986 at the Department of Medical Biochemistry in Geneva

  • Maintained by the Swiss Institute of Bio-informatics (SIB) and funded by GeneBio

  • Few redundancies

  • Direct submission (from sequencing, not translation)

PIR

  • PIR (The Protein Information Resource) was created by M.O. Dayhoff in 1965

  • Maintained by many

  • In 2004, joined with other databases (Swiss-Prot and TrEMBL) to become part of the UniProt consortium


Protein data bank
Protein Data Bank language, etc.

  • Archive of 3-D structural data of biological macromolecules

  • Based on experimental data

  • Managed by the Research Collaboratory for Structural Bioinformatics (RCSB)

    • Rutgers & UCSD

  • As of January 11, 2012 contained 78477 structures

  • ~ 5000 membrane proteins

http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100



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