Bioinformatics for the classroom

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2 Οκτ 2013 (πριν από 4 χρόνια και 1 μήνα)

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Bioinformatics for your
classroom

Seth Bordenstein

Department of Biological Sciences

Vanderbilt University

NCBI

BLAST

1.

No programming skills needed

2.
Familiarity with personal computer
and internet browser

3.
Customizable and free

Advantages

Bioinformatics is like using ‘Google’ for DNA sequences

National Center for Biotechnology
Information (NCBI)

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

Sequence Records

(millions)

Total Base Pairs

(billions)

0

5

10

15

20

25

30

35

0

5

10

15

20

25

30

35

40

Sequence records

Total base pairs

Release 148: 45.2 million records




49.4 billion nucleotides


Average doubling time ≈ 14 months

’83 ’84 ’85 ’86 ’87 ’88 ’89 ’90 ’91 ’92 ’93 ’94 ’95 ’96 ’97 ’98 ’99 ’00 ’01 ’02 ’03 ’04 ’05 ’06

40

45

45

50

55

50

Growth of NCBI
-

GenBank

DNA

RNA

cDNA

ESTs

phenotype

DNA sequences

genomes

protein

sequence

databases

protein

Bioinformatics is NOT just information technology.

It can teach the central dogmas of molecular biology


Target database: Adjustable using the pull
-
down menu


A Traditional

GenBank Record

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 AY182241.2 GI:32265057

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, 84
-
94 (2004)

REFERENCE 2 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA

REFERENCE 3 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA


REMARK Sequence update by submitter

COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.

FEATURES Location/Qualifiers


source 1..1931


/organism="Malus x domestica"


/mol_type="mRNA"


/cultivar="'Law Rome'"


/db_xref="taxon:3750"


/tissue_type="peel"


gene 1..1931


/gene="AFS1"


CDS 54..1784


/gene="AFS1"


/note="terpene synthase"


/codon_start=1


/product="(E,E)
-
alpha
-
farnesene synthase"


/protein_id="AAO22848.2"


/db_xref="GI:32265058"


/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

Feature Table

Sequence

The Flatfile Format

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 AY182241.2 GI:32265057

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, 84
-
94 (2004)

REFERENCE 2 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA

REFERENCE 3 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA


REMARK Sequence update by submitter

COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.

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 AY182241.2 GI:32265057

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, 84
-
94 (2004)

REFERENCE 2 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA

REFERENCE 3 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA


REMARK Sequence update by submitter

COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.

Header: Locus Line

LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004

Molecule type

Division

Modification Date

Locus name

Length

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 AY182241.2 GI:32265057

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, 84
-
94 (2004)

REFERENCE 2 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA

REFERENCE 3 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA


REMARK Sequence update by submitter

COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.

Header: Database Identifiers

ACCESSION AY182241

VERSION AY182241.2 GI:32265057

Accession


Stable


Reportable


Universal

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 AY182241.2 GI:32265057

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, 84
-
94 (2004)

REFERENCE 2 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA

REFERENCE 3 (bases 1 to 1931)


AUTHORS Pechous,S.W. and Whitaker,B.D.


TITLE Direct Submission


JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,


USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD


20705, USA


REMARK Sequence update by submitter

COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.

Header: Organism

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

FEATURES Location/Qualifiers


source 1..1931


/organism="Malus x domestica"


/mol_type="mRNA"


/cultivar="'Law Rome'"


/db_xref="taxon:3750"


/tissue_type="peel"


gene 1..1931


/gene="AFS1"


CDS 54..1784


/gene="AFS1"


/note="terpene synthase"


/codon_start=1


/product="(E,E)
-
alpha
-
farnesene synthase"


/protein_id="AAO22848.2"


/db_xref="GI:32265058"


/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK


NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF


EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE


NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS


LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW


ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS


EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT


KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA


DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK


GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI


LSLLFQPLVN"

The Feature Table

Coding sequence

start (atg)

stop (tag)

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

//

BLAST:


Compare new genes to old ones


Compare genes from different species or
hosts


Investigate the transcriptome (cDNAs)


Identify possible functions based on
similarities to known sequences.

Query a database for sequences similar to an


input sequence.


GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <




>
C
T
A
G
A
G
A
G
C
-
G
T
A
G
T
C
AG
A
GTG
T
CTTTGAGTTCC


What are the broad goals of this lab?



To provide an introduction to bioinformatics
with a focus on NCBI



To introduce you to searching for articles,
sequences, scientists (perhaps yourself ;))



To use the most powerful and reliable
method to determine evolutionary
relationships between genes


To combine your
Wolbachia

research with
computational biology


What are the specific goals of this lab?



To look for brand new W strains



To make a phylogenetic tree of W



To ultimately compare the W tree to an
insect phylogeny to infer lateral vs. vertical
transmission of your W strains



To contribute to a national sequence
database on the genetic diversity of W 16S
rRNA gene

Outcomes: A New
Wolbachia

Species?


GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-

100%



GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-

100%



GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-

100%



GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-

100%


Insect Phylogeny

Top 5 Wolbachia BLAST matches


GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-

100%







Let’s Begin Our Bioinformatic Exercise
Lab 5