1. Bioinformatics for your classroom
No programming skills needed
Familiarity with personal computer and internet browser
Customizable and free
NCBI
BLAST
Seth Bordenstein
Discover the Microbes Within!
March 12, 2006

2. Bioinformatics is like using ‘Google’ for DNA sequences

3. Web Access: http://www.ncbi.nlm.nih.gov
NCBI homepage. Logo will take you back to home page.
About NCBI provides introduction to the NCBI and contains basic information on genetics and bioinformatics.

4. Web Access
Target database: Adjustable using the pull-down menu

5. Primary vs. Derivative Sequence Databases
Algorithms
UniGene
Curators
RefSeq
Genome
Assembly
TATAGCCG
AGCTCCGATA
CCGATGACAA GA
ATT C AT
TTGACA
ATTGACTA
ACGTGC
CGTGA
TATAGCCG
Labs
Sequencing
Centers
Updated
continually
by NCBI
~11,000 sequences are submitted per day.
GenBank
Updated ONLY
by submitters

6. Release 148: 45.2 million records 49.4 billion nucleotides50 55 45 50 40 45 35 40
Sequence records
Total base pairs 30 35
Release 148: million records
49.4 billion nucleotides
Average doubling time ≈ 14 months 30 25
Total Base Pairs
(billions)
Sequence Records
(millions) 25 20 20 15 15 10 10 5 5
’83 ’84 ’85 ’86 ’87 ’88 ’89 ’90 ’91 ’92 ’93 ’94 ’95 ’96 ’97 ’98 ’99 ’00 ’01 ’02 ’03 ’04 ’05 ’06

10. A Traditional GenBank Record
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
FEATURES Location/Qualifiers
source
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene
/gene="AFS1"
CDS
/note="terpene synthase"
/codon_start=1
/product="(E,E)-alpha-farnesene synthase"
/protein_id="AAO "
/db_xref="GI: "
/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK
NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF
EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE
DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK
GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI
LSLLFQPLVN"
ORIGIN
1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat
61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg
121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt
181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga
241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt //
Header
The Flatfile Format
Feature Table
Line-type identifier format.
Sequence

11. The Header LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:

12. Header: Locus Line Length Division Molecule type Locus name
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
LOCUS AY bp mRNA linear PLN 04-MAY-2004
Molecule type
Division
Modification Date
Locus name
Length
Locus line.

13. Header: Database Identifiers
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
Accession
Stable
Reportable
Universal
ACCESSION AY182241
VERSION AY GI:

14. NCBI-controlled taxonomy
Header: Organism
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons;
core eudicots; rosids; eurosids I; Rosales; Rosaceae;
Maloideae; Malus.
NCBI-controlled taxonomy
Portion of the record that NCBI controls. Retrieving sequences in precise and accurate way (useful for Entrez searching).

15. The Feature Table Coding sequence FEATURES Location/Qualifiers
source
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene
/gene="AFS1"
CDS
/note="terpene synthase"
/codon_start=1
/product="(E,E)-alpha-farnesene synthase"
/protein_id="AAO "
/db_xref="GI: "
/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK
NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF
EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE
NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS
LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW
ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS
EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT
KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA
DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK
GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI
LSLLFQPLVN"
start (atg)
stop (tag)
Coding sequence
Biologically interesting information.

16. The Sequence: What do you do with it?
ORIGIN
1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat
61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg
121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt
181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga
1741 ggacccacat cctgtcttta ctattccaac ctcttgtaaa ctagtactca tatagtttga
1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt
1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa
1921 aaaaaaaaaa a //
1/10,000 bp error ratio

17. Uses of BLAST: Query a database for sequences similar to an
input sequence.
Identify previously characterized sequences.
Find phylogenetically related sequences.
Identify possible functions based on similarities to known sequences.

18. The different versions of BLAST

20. Let’s Begin Our Bioinformatic Exercise!
Advantages of using an online exercise for Bioinformatics:
The real experience; Interactive for self-inquiry
Continuously updateable with suggestions
Links education with technology
Uses the computer - a friendly tool to students
Free and no supply costs if you have computers
You can start this tutorial on Monday!
Let’s Begin Our Bioinformatic Exercise!