A trip back in history

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A trip back in history
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Old World
We ran the process
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The New World
TGAGACACATATTTTTGATATTCCAGTTGTTGCAATC GAATGTAAAACA
TATTTAGATCTTTAAATGTATGGTAC ATTCAAGATCCAACCTTCATTCT
AGTGTTTAAAGAGAAC TGATTTGTTTGCAGGGGCAGGAGGCTTTGGTTT
AGGTTTTG AAATGGCAGGCTTCTCTGTACCTTTATCTGTTGAAATTGAT
ACCTGGGCTTGTGATACACTACGCTACAACCGCCCTGATTCAACAGTTAT
TCAAAATGATATCGGTAACTTTAGTACAGAAAATGACGTTAAGAATATCT
GCAACTTTAAACCTGATATTATTATTGGCGGGCCTCCATGCCAGGGATTT
AGTATTGCTGGGCCAGCCCAAAAAGATCCTAAAGATCCTAGAAATGGTTT
ATTCATCAACTTTGCACAATGGATAAAATTTCTTGAACCTAAAGCGTTTG
TCATGGAAAACGTAAAAGGATTGCTATCAAGGAAAAATGCAGAAGGTTTT
AAAGTTATAGATATTATTAAGAAAACATTTGAAGAACTTGGTTATTTTGT
CGAAGTATGGGTTTTAAATGCTGCGGAATATGGCATTCCGCAAATTAGAG
AACGTATTTTTATTGTTGGCAATAAAAAAGGTAAAGTACTAGGTATTCCT
AAAAAAACACATTCTCTGCAATTTTTAAATTTAAATAGGTCTCAATTATC
GATCTTCGATGATATGAGTATTATACCTGCACTAACTTTGTGGGACGCAA
TATCAGACTTACCAGAACTTAATGCGCGTGAAGGAAGTGAAGAGCAACCC
TATCATTTAAAACCTCAAAATACTTATCAGACTTGGGCTAGAAATGGTAG
TGCTACGCTTTACAATCATGTTGCAATGGAACATTCTGACCGTTTAGTAG
AACGTTTCCGGCATATAAAATGGGGTGAATCCAGTTCGGATGTATCTAAA
GAACATGGAGCTAGACGACGTAGTGGTAATGGTGAATTATCAAACAAATC
ATATGATCAGAATAATCGCCGTTTAAATCCTCATAAACCGTCTCACACTA
TTGCTGCGTCATTCTATGCTAATTTTGTCCATCCTTTTCAACATCGAAAT
TTAACAGCCCGTGAAGGAGCTAGAATCCAATCTTTTCCAGATAACTATAG
ATTTTTTGGAAAAAAAACTGTCGTATCTCATAAACTATTGCATCGAGAAG
AAAGATTTGATGAAAAATTTCTTTGTCAATATAATCAAATCGGTAATGCT
GTACCCCCTCTTCTCGCTAAAGTAATTGCACATCATCTTCTAGAGAAATT
AGAGTTATGCCAACAACTGATAGAAATCCTCTAGTGCATGGATCAAATCT
TGAACAAAAAGAGAATCATCGTACAAAATACAGAGATACTGAAAGCAGGA
CTTTCCTTAGAGAAATCAGAACTGAATATGACAAATGGCATAAAGCAAAT
ATGAACCTGGTTGGACCAAAATCAGAAATTACTGACCAAGATGATTCAAT
TATTACTCAAAGAGTGGAACTTCTCACTAAATATAAAGATTTTTTAGATC
AGCAGCATTATGCAGAAAAATTTGATTCAAGATCCAACCTTCATTCTAGT
GTTTTAGAGACCATTTATAAAGTAAATCTTTAGACGACTAGACGACGTAG
CATAATACGAGTCATAACGGCATATATGGCAGCCTCACTCATTTCTGGGA
GACGCTCATAATCCTTACTGAGACGACGGTACTGGTTTAACCAGCCAAAT
GTTCTTTCTACTACCCACCGTTTGGGCAAAACCTGAAATTCTTGATTAGT
ACGCCGGATTACCTCAACATGAGCTTGAATCATCAGCCAAACAGAGAGCG
CAAATTTATCACCGTCATAGCCGGAATCAACCCAGATGACTTCAACTTTT
TCCAGTAATTCTGGACGCTCTTCTAACAGTTCCATCAAAGTATAGGCGGC
AAGTAATCTTTCTCCAGCATTTGCTTCACTTACAACCACTTTTAACAAAA
GTCCCAGACTATCAACCAAAGTTTGCCGCTTTCGTCCTTTTACCTTCTTG
CCACCATCAAAACCGTACACATCCCCCTTTTTTCAGTCGTTTTTACCGAC
TGGCTGTCTGCCGCGATCGCCGTGGGTTGAGTTGACTTCCCCATTTTTTG
ACGAACTTGATCGCGCAAAGTATGATTCATTTCAGTTGAACTAGGAGGAA
AATCCCCTGGAAGCATATCCCACTGACAACCTGTTTTCAGATGGTAGTAG
ATAGCGTTGCATACTTCTCGCATATCAGTTGTTCGGGGATGCCCACCGCA
TTTAGCGGGTGGAATCAAAGGAGCTAAAATTGCCCATTCTGAGTCATTAA
GGTCTGTAGAATAAGACTTTCGTCTCATTGTTTCCTATGTAAATACACTC
TACAAACAGTATCTTATCGCTGCCTTTTTATCTTAGCTCTCCTTTAGATT
TACTTTATAAATAGCCTCTTAGAAGAATTTCTTTATTATTTATTTAAAGA
TTTAGTACAAGATTTCGGGCAGAACGCTCTTATTGGTAAGTCACACACGT
TCAAAGATATTTTCTTCGTACCACCAAAATATTCTGAAATGCTCAAGCGA
CCTTATGCGCGAATTGAGAGAAAAGATCATGATTTCGTAATTGGTGCAAC
TGTTCAAGCATCGCTTGAAGCAGCACCTCCTCCAGAACAAAACCATGCTT
GAGGGATCTTCACGCGCAGCAGAGGATTTAAAAGCGAGAAATCCTAACAG
TTTATACCTTGTGGTTATGGAATGGATAAAACTGACCAATGATGTAAATT
TACGAAAATATAAAGTTGATCAAATTTATGTACTACGTCAGCAAAAAAAT
ACTGATAGAGAGTTTAGGTATGAGTCAACTTACATAAAAAAT
9
The New World
AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTT
TGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGA
CCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACC
TTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTT
CCTCTAGAATACCGAGGGCATCTTGAAATGTATCAGGATAACCAACCTGG
TCTCCAGGAGCAAAATAAGCAACTTTTTTGCCGATGAAGTCAATGTTATC
TAACTCATCATAAAAATTTTCCCAATCACTTTGCAATTCTCCAACATTCC
AGGTAGGACAACCAACAACGATATAATCGTAGTTATTGAAATCACTTGGT
TCAGCTTGTGAAATATCATATAAAGTTACAACACTATCACCACCAAACTC
CTTCTGAATTATTTCTGATTCAGTTTGGGTATTGCCTGTTTGAGTACCAA
AAAATAAACCAATATTAGACATTTTTACTCCTTTTATGTATTTGCAAAAT
TATTTCAATTAAAATATTTAGTAATAATTAATTGTTAGCTAGCTAATAAT
TAAATTTTTATTACAATCATTGTAAAAGGCATTGAAAAAGTAAATAAAAA
TTTTTATTCTACGTTATTTCAAAAATATTTACTTACATATACTTAACCTT
TATAGTGATGTAATATACTCTAATTCCTATTTTACTTATAAATACCATCT
CAGCTTAATGTAACGAATTTTTCTGTTTATCTTTAAATACAAAAAATTCA
ACAAAACTACAGAAAATTAATCTTAATAACACAAAACAAGTATCAATCTG
TAATACAACTAAGCTTAAATAAATTAATAGAAAGCTTCATCTATCTAATA
GGTTGAGAATAGTTTATGTCTAATGACATAAATTCATTCGTGTTGATTTC
ATTTGGGTATATTCATCTGATTTAGGATTTACTCCATTAAGTTTGTACTC
ATCAATGCCCGCCTGTTGGTATCCACAATTCTCATACAGTGCGCGAGCAA
AGTAATCAATCGTTCGTCGCCATATCTAACTTTGAGTCAAACAAACCAGT
TGGATTACCAACCCTCAACTAATCGCTTCTTTAAGGCGAGCGATCGCACA
TTTAACTGTTGGTTGTCACAAGAGAACTAATACTACAGCAGTATATTTAA
CAACTAAGGGTGGTTCAACTTTCGCTGCGACTCCTCCAACGCGCTGAAAT
ACACAGGACTGATGCGATCGCAAACTCTTTGACTAAATTCCATACATTAT
CATGACCATCTCCCAAACAAACAAGTGGGTTAACCAGATGCTGACTATTA
ACATCCCCTGAGTTCGGAGTTGTAGGTCTATTTGACTGGTTCAAAGCGAT
GATGGAACGGCTTTGTTGCATGAATTAAAAAAAGACACACCATCACCTAC
TTCTAGGATAGACACATCAAACGTCCCACCGCCTAAGTCAAATACCAAGA
TAATTTCGTTAGTTTTCTTGTCAAGTCCGTAAGCGAGGGCCGCCGCCGTG
GGCTAGTTGATAATTCGCAGAACTTTAATCCCGGCAATTCTACTGGCATC
TTTGGTAGCCTGCCGTTGAGAGTCATTGAAATAGGCAGGGGTGGTAATTA
CCGCTTGCCTCACTGGTTCCCCCAGATATGTGCTGGCATCATCTATCAGC
TTGCGGACTACCTCATACCATTTCACGAAAAACCTGATACACATGTAAAC
TCTGAAACCCTTGCTGTATCAAAGTTTTGTAATTACGAATTACGAATTAC
GAATTGATATCAGCCGAGATTTCTTCGGGTGAAAATTCCTTGTTCAGAGC
GGGACAGTGTAGCTTGACATTGCCATTACTGTCACGTACCACTTTGTAAG
TAACTTGTTTTGCCTCTTGCGTAACTTCATCATACCTGCGCCCGATGAAC
CGCTTCACAGAATAAAAAGTGTTTTCTGGGTTCATTACACCCTGGCGCTT

What have we lost?
10
The New World
What have we lost?
What have we lost?
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Observation and Filters
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation and Filters
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation and Filters
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation and Filters
Photos courtesy of www.webshots.com and Peter
Smallwood
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Experiment
Photos courtesy of www.webshots.com and Peter
Smallwood
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Filters Information reducersSquirrel filter
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Filters Information reducersMolecule filter
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Filters Information reducersSequence filter
How organism is made How organism works
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Filters Information reducersGene finders
e.g. Glimmer, GeneMark,
gi22967278gbZP_00014872.1 hypothetical
protein Rhodospirillum rubrum
Length 367 Score 64.3 bits (155), Expect
2e-09 Identities 68/296 (22), Positives
123/296 (41), Query 25 VYLGDCLEIIKSIPDNSVNLIL
TSPPFALTRKKEYGN--------- Y GD
ESP SI PP E
Sbjct 10 IYQGDSIEVMRSLPSASIDMIFADPPYNMMLGGELLRP
DNSRVDYA
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Filters Information reducersGene finders
e.g. Glimmer, GeneMark,
Hidden Markov model
gi22967278gbZP_00014872.1 hypothetical
protein Rhodospirillum rubrum
Length 367 Score 64.3 bits (155), Expect
2e-09 Identities 68/296 (22), Positives
123/296 (41), Query 25 VYLGDCLEIIKSIPDNSVNLIL
TSPPFALTRKKEYGN--------- Y GD
ESP SI PP E
Sbjct 10 IYQGDSIEVMRSLPSASIDMIFADPPYNMMLGGELLRP
DNSRVDYA
Predicted genes
Candidate genes
24
Filters Information reducersGene finders
e.g. Glimmer, GeneMark,
Hidden Markov model
Conform to standard model
Challenge accepted beliefs
gi22967278gbZP_00014872.1 hypothetical
protein Rhodospirillum rubrum
Length 367 Score 64.3 bits (155), Expect
2e-09 Identities 68/296 (22), Positives
123/296 (41), Query 25 VYLGDCLEIIKSIPDNSVNLIL
TSPPFALTRKKEYGN--------- Y GD
ESP SI PP E
Sbjct 10 IYQGDSIEVMRSLPSASIDMIFADPPYNMMLGGELLRP
DNSRVDYA
Predicted genes
Candidate genes
Predicted genes
25
Computers are powerful
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Computers are tempting
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Computers are tempting
Globin
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Crisis in Bioinformatics
1. Need high-level filters
v
29
Crisis in Bioinformatics
1. Need high-level filters
v

2. Need access to raw phenomena
30
Crisis in Bioinformatics
1. Need high-level filters
v

2. Need access to raw phenomena
?
3. Need new tools for new phenomena
31
Crisis in Bioinformatics
1. Need high-level filters
v

2. Need access to raw phenomena
?
3. Need new tools for new phenomena
?
4. Need intuitive representation of results
32
Crisis in Bioinformatics
1. Need high-level filters
v

2. Need access to raw phenomena
?
3. Need new tools for new phenomena
?
4. Need intuitive representation of results
?!?
5. Need ability to do this ourselves
How?
33
Prochlorococcus MED4
Prochlorococcus MIT9313
34
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

35
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Click to initiate stepsto bring
together items (sequences, orfs, data, etc)
that you will specify
Build set
36
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
37
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Consider set... (loop) IF... THEN... OTHERWISE
Consider set... (loop)
38
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Choose set type
Choose database
Consider each item in
All nucleotides of All open reading frames of All
amino acid sequences of All intergenic regions
of Human-annotated orfs of Private set Public set
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH Synechocystis PCC
6803 Thermosynechococcus Trichodesmium Unicellulul
ar Filamentous All
All open reading frames of
39
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Choose database
Consider each item in
All open reading frames of
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH Synechocystis PCC
6803 Thermosynechococcus Trichodesmium Unicellulul
ar Filamentous All
Prochlorococcus MED4
40
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
41
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

v

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

42
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
Click to give a value to a new or
old variable Click to access
results of experiments Click to
see list of available statements Click
to see list of available manipulations Click
to see statements to manipulate
sets
Variable
Data
Operation
Function
Set operation
43
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Consider set... (loop) IF... THEN...
OTHERWISE KEEP item DISCARD item
IF... THEN... OTHERWISE

Consider each item in
All open reading frames of
Prochlorococcus MED4
44
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
Click or
to begin specifying condition to be met
Variable
Data
Function
IF
45
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Ortholog of Protein product of Sequence
of Upstream region of Downstream region of
Ortholog of

Consider each item in
All open reading frames of
Prochlorococcus MED4
IF
46
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
Variable
Choose database
( in
)
IF
ItemSpecify
Ortholog of
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH8102 Synechocystis PCC
6803 Thermosynechococcus Trichodesmium
Item
47
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
Choose database
( in
)
IF
Item
Ortholog of
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH8102 Synechocystis PCC
6803 Thermosynechococcus Trichodesmium
Prochlorococcus MIT9313
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Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
? exists doesnt exist

Consider each item in
All open reading frames of
Prochlorococcus MED4
doesnt exist
( in
)
IF
Item
Ortholog of
Prochlorococcus MIT9313
Click specific operation to continue specifying
the condition to be met or click
to save results of function
Variable
49
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
AND OR BUT NOT IF... THEN... OTHERWISE

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
)
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
Click a logical operation to continue specifying
the condition to be met or IF... THEN... to
end the condition
50
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

v

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

v

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

51
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
AND OR BUT NOT IF... THEN... OTHERWISE
AND

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
)
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
Click a logical operation to continue specifying
the condition to be met or IF... THEN... to
end the condition
52
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
)
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
Click or
to continue specifying condition to be met
Variable
Data
Function
53
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
Ortholog of Protein product of Sequence
of Upstream region of Downstream region of
Ortholog of

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
)
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
54
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
Variable
Choose database
( in
)
ItemSpecify
Ortholog of
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH8102 Synechocystis PCC
6803 Thermosynechococcus Trichodesmium
Item
55
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
Choose database
( in
)
Item
Ortholog of
Arthrobacter platensis Gloeobacter
violaceus Microcystis aeruginosa Nostoc
punctiforme Nostoc PCC 7120 Prochlorococcus
MED4 Prochlorococcus MIT9313 Prochlorococcus
S120 Synechococcus PCC6301 Synechococcus
PCC7942 Synechococcus WH8102 Synechocystis PCC
6803 Thermosynechococcus Trichodesmium
Synechocystis PCC6803
56
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
? exists doesnt exist

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
Click specific operation to continue specifying
the condition to be met or click
to save results of function
Variable
57
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
Type variable name
)
(assigned to
6803 ortholog
58
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
? exists doesnt exist

Consider each item in
All open reading frames of
Prochlorococcus MED4
exists
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
)
(assigned to
6803 ortholog
Click specific operation to continue specifying
the condition to be met or click
to save results of function
Variable
59
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
AND OR BUT NOT IF... THEN... OTHERWISE

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
exists
)
(assigned to
6803 ortholog
Click a logical operation to continue specifying
the condition to be met or IF... THEN... to
end the condition
60
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

v

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

v

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

v

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

61
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done
AND OR BUT NOT IF... THEN... OTHERWISE
AND

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
exists
)
(assigned to
6803 ortholog
Click a logical operation to continue specifying
the condition to be met or IF... THEN... to
end the condition
62
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
Click or
to continue specifying condition to be met
Variable
Data
Function
63
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
Variable
Choose organism used
data for
in
Item6803 ortholog Specify
Microcystis aeruginosa Nostoc punctiforme Nostoc
PCC 7120 Prochlorococcus MED4 Prochlorococcus
MIT9313 Prochlorococcus S120 Synechococcus
PCC6301 Synechococcus PCC7942 Synechococcus
WH8102 Synechocystis PCC 6803
6803 ortholog
64
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
Choose organism used
data for
in
6803 ortholog
Microcystis aeruginosa Nostoc punctiforme Nostoc
PCC 7120 Prochlorococcus MED4 Prochlorococcus
MIT9313 Prochlorococcus S120 Synechococcus
PCC6301 Synechococcus PCC7942 Synechococcus
WH8102 Synechocystis PCC 6803
Synechocystis PCC 6803
65
Display set
Build set
Cancel
HELP
Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
Choose type
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray 2D gel
microarray
66
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Set operation
Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
High light vs low light experiment
)
(assigned to
6803 ortholog
Choose expt
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1 Suzuki1 Yoshimura1
Hihara1
67
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or exists doesnt exist

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist

( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
68
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Variable
Data
Operation
Function
Done

Consider each item in
All open reading frames of
Prochlorococcus MED4
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
Value

2
69
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AND OR BUT NOT IF... THEN... OTHERWISE

Consider each item in
All open reading frames of
Prochlorococcus MED4
IF... THEN... OTHERWISE
( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
Value

2
Click a logical operation to continue specifying
the condition to be met or IF... THEN... to
end the condition
70
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( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
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sets
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( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
72
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( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
Variable
Type name of set
Add
to
Item6803 ortholog Specify
6803 ortholog
73
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( in
AND
IF
Item
Ortholog of
Prochlorococcus MIT9313
doesnt exist
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
Type name of set
Add
to
6803 ortholog
Light-specific genes
74
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)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
Type name of set
Add
to
6803 ortholog
Light-specific genes
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results of experiments Click to
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to see list of available manipulations Click
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sets
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75
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

v

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

v

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

v

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

76
How do cells control response to light?
What genes are related to the adaptation to high
light?
Look for

• Gene present in Prochlorococcus MED4 MED4 is
  naturally adapted to grow in high light.

v

• Ortholog absent in Prochlorococcus MIT9313
  MIT9313 is naturally adapted to grow in low light

v

• Ortholog present in Synechocystis PCC 6803
  Reason will become apparent in a moment

v

• Synechocystis PCC 6803 ortholog responds to high
  light Gene turns on by factor 2 in response
  to high light

v
77
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( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
Type name of set
Add
to
6803 ortholog
Light-specific genes
Click to give a value to a new or
old variable Click to access
results of experiments Click to
see list of available statements Click
to see list of available manipulations Click
to see statements to manipulate
sets
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78
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Done
Save results and scriptSave only results
Save results and script
( in
)
Item
Ortholog of
Synechocystis PCC 6803
AND
exists
)
(assigned to
6803 ortholog
data for
in
6803 ortholog
Synechocystis PCC 6803
microarray
Hihara1
THEN

2
Type name of set
Add
to
6803 ortholog
Light-specific genes
79
Equivalent script that bypasses interface
(loop for item in (Genes ProcMed4) as
all-orthologous
(all-blast-orthologous-geneIDs item stdevalue)
as 6803ortholog (Genes Syny6803) in
all-orthologous) as light-specific-genes
nil when (and (there-are-not-any
member-geneID-of-gene-frames
(Genes slotv Proc9313) in
all-orthologous))
(there-are-any 'member-geneID-of-gene-frames
6803ortholog)
( ratio-value
(select-matching-geneIDs-from-table
Hihara1 item) 2))))
collect light-specific-genes 6803ortholog)
80
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Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
81
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Synechocystis PCC 6803 slr1332
Replicon Chromosome Coordinates 1670650
(start-ATG) 1671864 (stop) Human Length
404 amino acids Strand Direct Gene name(s)
fabF or fabJ Function beta-ketoacyl-acyl carrier
protein synthase Human Activity In vivo
activity exists Experiment Orthologs
A
A
A
Syny6803slr1332
110-89
NostPun611.025
Anab7120alr4255
310-87
82
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Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
What to do with this set?

• Function of genes?

• Regulation of genes?

- Add first genes of putative operons
83
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Display set
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Set operation
ADD TO DELETE FROM UNION OF INTERSECTION
OF Arithmetic
ADD TO
Operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
84
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Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
Add to set
Find specific gene Add set of genes Specify
gene Click on icon of gene
85
Build set
Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
Add to set
Find specific gene Add set of genes Specify
gene Click on icon of gene
86
Build set
Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1331 Processing protease
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0576 Putative
epimerase/hydratase
Add to set
Find specific gene Add set of genes Specify
gene Click on icon of gene
87
Build set
Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1331 Processing protease
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0788 Hypothetical protein
Syny6803sll0576 Putative
epimerase/hydratase
Add to set
Find specific gene Add set of genes Specify
gene Click on icon of gene
88
Build set
Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1331 Processing protease
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0788 Hypothetical protein
Syny6803sll0576 Putative
epimerase/hydratase
What to do with this set?

• Function of genes?

• Regulation of genes?

- Add first genes of putative operons
- Remove genes within putative operons
89
Build set
Display set
Done
HELP
Set operation
ADD TO DELETE FROM UNION OF INTERSECTION
OF Arithmetic
Set Light-specific genes
DELETE FROM
Syny6803sll0990 Formaldehyde
dehydrogenase (glutathione dependent)
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1331 Processing protease
Syny6803slr1332 fabF beta ketoacyl acyl
carrier protein synthase
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0789 Response regulator
(OmpR)
Syny6803sll0788 Hypothetical protein
Syny6803sll0576 Putative
epimerase/hydratase
What to do with this set?

• Function of genes?

• Regulation of genes?

- Add first genes of putative operons
- Remove genes within putative operons
90
Build set
Display set
Done
HELP
Set operation
Set Light-specific genes
Syny6803srl7009 trnR tRNA Arg (UCU)
Syny6803slr1331 Processing protease
Syny6803sll0337 Sensor histidine
kinase
Syny6803sll0335 Hypothetical
Syny6803sll0788 Hypothetical protein
Syny6803sll0576 Putative
epimerase/hydratase
What to do with this set?

• Function of genes?

• Regulation of genes?

- Add first genes of putative operons
- Remove genes within putative operons
- Find common upstream elements (Meme)
91
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92
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Data
Operation
Function
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Ortholog of Protein product of Sequence
of Upstream region of Downstream region of Common
sequences(Meme) of
Upstream region of
93
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Choose set
Type variable name
Upstream region of
assigned to
Light-specific genes Public set
Light-specific genes
94
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Variable
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Type variable name
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
95
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Variable
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Type variable name
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
96
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Variable
Data
Operation
Function
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Ortholog of Protein product of Sequence
of Upstream region of Downstream region of Common
sequences(Meme) of
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
Common sequences(Meme) of
97
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Variable
Data
Operation
Function
Done
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
Choose set
Type variable name
Common sequences of
assigned to
Light-specific genes Upstream light-sp
genes Public set
Upstream light sp-genes
98
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Variable
Data
Operation
Function
Done
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
Type variable name
Common sequences of
assigned to
Upstream light-sp genes
Memed light-sp genes
99
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Variable
Data
Operation
Function
Done
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
Type variable name
Common sequences of
assigned to
Upstream light-sp genes
Memed light-sp genes
100
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Light-specific genes Upstream light-sp
genes Memed light-sp genes Public set
Variable
Data
Operation
Function
Done
Memed light sp-genes
Upstream region of
assigned to
Light-specific genes
Upstream light-sp genes
Type variable name
Common sequences of
assigned to
Upstream light-sp genes
Memed light-sp genes
101
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Set Memed upstream light-sp genes
Len Pos E-val Left flank
Motif Right flank  
Upstream of Syny6803srl7009 638 D 509 6.38e-05 AA
ATATGGGA GAATGGAA TTGAGTAGCA
Upstream of Syny6803slr1331 159 D 152 4.38e-05 GG
CCCATGGG GACTAGGA
Upstream of Syny6803sll0337 138 D
34 3.29e-05 AGCTTAAAAA GACTAGAA TTCAATGGGT
Upstream of Syny6803sll0335 279 D 183 5.30e-05 AA
GGGTTAGC GACTGGAG TTGGCAAAAC
Upstream of Syny6803sll0788 221 D 184 1.09e-05 TG
CTTTGCCA GACTGGAA TTAGAGAAGG
Upstream of Syny6803sll0576 79 D
28 1.31e-04 TTTTTTGCTT TACTGGGA ACGGATATTT
102
What have we done?

• Drawn on complex knowledge base

• Combined multiple tools

• Written a computer program

• Modified set by hand

Did it ourselves
103
What havent we done?

• Examined unfiltered reality

104
(No Transcript)
105
(No Transcript)
106
Display of gene context by TIGR/CMR (or Kazusa)
Nostoc sp. PCC 7120 Position Search and Segment
Retrieval
Nostoc sp. PCC 7120 3455501-3456500
ttagtagatgggcttgatgtacagtactttgaaatcaattccctccgccg
caaaatggct gtagttagtcaagatacatttattttcaacacttctatt
agagacaatatcgcctacggt acatctggggcgagtgaagcggaaatta
gagaagtagcgcggctagcaaatgcgttgcaa
tttatcgaagaaatgcccgaagggtttgatactaagttaggcgatcgcgg
tgtccgttta tctggaggacagagacaacggattgcgatcgctcgtgca
ttactccgagatcccgaaatc ctcattcttgacgaagccaccagcgccc
tagattcagtctccgagcgattaattcaggag
tctatagaaaaactttccgtgggtagaacagtaattgcgatcgctcacag
actctccaca attgccaaagcagataaggttgtggtgatggaacaaggg
cgaattgttgagcagggaaat tatcaagaacttctagaacaacgcggaa
agctctggaaatatcaccagatgcaacacgaa
tcaggacagactaattcgtaatatcaattcaaaattcaaaattcaaaatt
caaaattagg gaagccgagcagaatcatggttttggggtatgtatctgt
cccattcttttttcaaatcgg tataactccccaatccccaatccccaat
ctccagtccccaatccccaatccccaatcccc
aatccccagtccccaatccccaatcccatgaaaatttccgtcatcatctc
gaattacaac tatgctcgttatctttctagagcaatcaactctgttctc
gctcaaactcactcagacatt gaaatcgttatcgtagatgatggttcta
cagataacagccgtgatgttattacccaactg
caagaacaagcaccggataaaatcaagcccatctttcaagcaaatcaagg
acagggaggc gctttcaatgcggggtttgcggcggcgactggcgaagtc
g
107
Display of gene context by Artemis
108
Display of gene context by TAIR
109
Anabaena Chromosome (6413771 bp) 3455501-3456500
.............................................
alr2835hepA ABC transport3454238 -
3456061 alr2836 glycosyltransferase 3456248 -
3457216
TTAGTAGATGGGCTTGATGTACAGTACTTTGAAATCAATTCCCTCCGCCG
CAAAATGGCTGTAGTTAGTCAAGATACATTTATTTTCAACACTTCTATT
A GAGACAATATCGCCTACGGTACATCTGGGGCGAGTGAAGCGGAAATTA
GA GAAGTAGCGCGGCTAGCAAATGCGTTGCAATTTATCGAAGAAATGCC
CGA AGGGTTTGATACTAAGTTAGGCGATCGCGGTGTCCGTTTATCTGGA
GGAC AGAGACAACGGATTGCGATCGCTCGTGCATTACTCCGAGATCCCG
AAATC CTCATTCTTGACGAAGCCACCAGCGCCCTAGATTCAGTCTCCGA
GCGATT AATTCAGGAGTCTATAGAAAAACTTTCCGTGGGTAGAACAGTA
ATTGCGA TCGCTCACAGACTCTCCACAATTGCCAAAGCAGATAAGGTTG
TGGTGATG GAACAAGGGCGAATTGTTGAGCAGGGAAATTATCAAGAACT
TCTAGAACA ACGCGGAAAGCTCTGGAAATATCACCAGATGCAACACGAA
TCAGGACAGA CTAATTCGTAATATCAATTCAAAATTCAAAATTCAAAAT
TCAAAATTAGG GAAGCCGAGCAGAATCATGGTTTTGGGGTATGTATCTG
TCCCATTCTTTT TTCAAATCGGTATAACTCCCCAATCCCCAATCCCCAA
TCTCCAGTCCCCA ATCCCCAATCCCCAATCCCCAATCCCCAGTCCCCAA
TCCCCAATCCCATG AAAATTTCCGTCATCATCTCGAATTACAACTATGC
TCGTTATCTTTCTAG AGCAATCAACTCTGTTCTCGCTCAAACTCACTCA
GACATTGAAATCGTTA TCGTAGATGATGGTTCTACAGATAACAGCCGTG
ATGTTATTACCCAACTG CAAGAACAAGCACCGGATAAAATCAAGCCCAT
CTTTCAAGCAAATCAAGG ACAGGGAGGCGCTTTCAATGCGGGGTTTGCG
GCGGCGACTGGCGAAGTCG
3455501 3455551 3455601 3455651 3455701 3455751
3455801 3455851 3455901 3455951 3456001 3456051
3456101 3456151 3456201 3456251 3456301 3456351
3456401 3456451
Alternate starts Annotated features Local
features Tandem repeats Inverted repeats Base
symbols
Base symbols
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
110
Anabaena Chromosome (6413771 bp) 3455501-3456500
.............................................
alr2835hepA ABC transport3454238 -
3456061 alr2836 glycosyltransferase 3456248 -
3457216
TTAGTAGATGGGCTTGATGTACAGTACTTTGAAATCAATTCCCTCCGCCG
CAAAATGGCTGTAGTTAGTCAAGATACATTTATTTTCAACACTTCTATT
A GAGACAATATCGCCTACGGTACATCTGGGGCGAGTGAAGCGGAAATTA
GA GAAGTAGCGCGGCTAGCAAATGCGTTGCAATTTATCGAAGAAATGCC
CGA AGGGTTTGATACTAAGTTAGGCGATCGCGGTGTCCGTTTATCTGGA
GGAC AGAGACAACGGATTGCGATCGCTCGTGCATTACTCCGAGATCCCG
AAATC CTCATTCTTGACGAAGCCACCAGCGCCCTAGATTCAGTCTCCGA
GCGATT AATTCAGGAGTCTATAGAAAAACTTTCCGTGGGTAGAACAGTA
ATTGCGA TCGCTCACAGACTCTCCACAATTGCCAAAGCAGATAAGGTTG
TGGTGATG GAACAAGGGCGAATTGTTGAGCAGGGAAATTATCAAGAACT
TCTAGAACA ACGCGGAAAGCTCTGGAAATATCACCAGATGCAACACGAA
TCAGGACAGA CTAATTCG?????????????????
??????? ??????????????????????
? ??????????????
??? ???????????
??ATG AAAATTTCCGTCATCATCTCGAATTACAACTATGC
TCGTTATCTTTCTAG AGCAATCAACTCTGTTCTCGCTCAAACTCACTCA
GACATTGAAATCGTTA TCGTAGATGATGGTTCTACAGATAACAGCCGTG
ATGTTATTACCCAACTG CAAGAACAAGCACCGGATAAAATCAAGCCCAT
CTTTCAAGCAAATCAAGG ACAGGGAGGCGCTTTCAATGCGGGGTTTGCG
GCGGCGACTGGCGAAGTCG
3455501 3455551 3455601 3455651 3455701 3455751
3455801 3455851 3455901 3455951 3456001 3456051
3456101 3456151 3456201 3456251 3456301 3456351
3456401 3456451
Alternate starts Annotated features Local
features Tandem repeats Inverted repeats Base
symbols
Tandem repeats
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
111
Anabaena Chromosome (6413771 bp) 3455501-3456500
.............................................
alr2835hepA ABC transport3454238 -
3456061 alr2836 glycosyltransferase 3456248 -
3457216
TTAGTAGATGGGCTTGATGTACAGTACTTTGAAATCAATTCCCTCCGCCG
CAAAATGGCTGTAGTTAGTCAAGATACATTTATTTTCAACACTTCTATT
A GAGACAATATCGCCTACGGTACATCTGGGGCGAGTGAAGCGGAAATTA
GA GAAGTAGCGCGGCTAGCAAATGCGTTGCAATTTATCGAAGAAATGCC
CGA AGGGTTTGATACTAAGTTAGGCGATCGCGGTGTCCGTTTATCTGGA
GGAC AGAGACAACGGATTGCGATCGCTCGTGCATTACTCCGAGATCCCG
AAATC CTCATTCTTGACGAAGCCACCAGCGCCCTAGATTCAGTCTCCGA
GCGATT AATTCAGGAGTCTATAGAAAAACTTTCCGTGGGTAGAACAGTA
ATTGCGA TCGCTCACAGACTCTCCACAATTGCCAAAGCAGATAAGGTTG
TGGTGATG GAACAAGGGCGAATTGTTGAGCAGGGAAATTATCAAGAACT
TCTAGAACA ACGCGGAAAGCTCTGGAAATATCACCAGATGCAACACGAA
TCAGGACAGA CTAATTCG?????????????????
??????? ??????????????????????
? ??????????????
??? ???????????
??ATG AAAATTTCCGTCATCATCTCGAATTACAACTATGC
TCGTTATCTTTCTAG AGCAATCAACTCTGTTCTCGCTCAAACTCACTCA
GACATTGAAATCGTTA TCGTAGATGATGGTTCTACAGATAACAGCCGTG
ATGTTATTACCCAACTG CAAGAACAAGCACCGGATAAAATCAAGCCCAT
CTTTCAAGCAAATCAAGG ACAGGGAGGCGCTTTCAATGCGGGGTTTGCG
GCGGCGACTGGCGAAGTCG
3455501 3455551 3455601 3455651 3455701 3455751