Analysis: Tools for directly examining sequence

1
Scenario 6
Analysis Tools for directly examining sequence
What follows is a simulation of the proposed
sequence interface. A PC-based prototype exists,
but the interface has not yet been ported to the
web. As you go through the simulation please
consider what capabilities you would want to
serve your research and annotation interests. A
narrative to help you go through the simulation
appears in a red-bordered box, such as the one
below.
To begin1. Click on Slide Show, (on the upper
toolbar)2. Click View Show3. Click Continue
button
Continue
2
Scenario 6
Analysis Tools for directly examining sequence
Youre intrigued by the motif you found in front
of Anabaena PCC 7120 all4312 and its
cyanobacterial orthologs (see Scenarios 1 and 5).
Youd like to look more deeply into it, by
examining the sequence near the orf. Youre not
sure what youre looking for, and youre open for
anything.
Continue
3
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Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs NostPunc
TricEryt Syny6803 TherElon
Lawrence/Collier conserved motif set
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Scenario 1 left us with the provocative finding
that all five cyanobacterial orthologs of all4312
are preceded by the same motif. What is that
motif and what might it mean? To answer that
question, click on the coordinates of all4312 to
get to the sequence interface.
Syny6803sll1330
TherElontlr1330
4
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
The interface places you in the Anabaena
chromosome in the region surrounding all4312,
with the orf highlighted as a block. Clicking on
all4312 would get us back to the annotation page.
Our goal was to look at the motif preceding the
orf, so click on Display.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
5
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
We want to display the motif predicted by
Lawrence/Collier, so click on Predicted features.
Alternate starts Annotated features Predicted
features Private features Tandem repeats Inverted
repeats Base symbols Invert display
Predicted features
Contig GoTo Block Find Display
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6
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
I was hoping to see sequences I recognized, but
thats made more difficult by the orf being on
the wrong strand. I could invert the entire
display, but instead Ill just work on a segment.
Click Block.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
7
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
The highlighted orf sequence could now be
downloaded or first translated then downloaded,
but Im interested now only in the region
preceding the gene. Click Define, in order to
highlight a new block of sequence.
DefineInvertTranslateSave Tools
Define
Contig GoTo Block Find Display
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8
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
Define the beginning of the block by clicking on
base 5167751 (4th line up). Then click on the
last base on the page (lower right corner).
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
9
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
Now that the bottom four lines are blocked, Click
on Block and then Invert.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
10
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
Now that the bottom four lines are blocked, Click
on Block and then Invert.
DefineInvertTranslateSave Tools
Invert
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
11
Anabaena Chromosome (6413771 bp) 5167950-5967751
(inverted)
.............................................
AACTATAACAAAAATTTAATAATATTATCAACTTCGCTCTGGACAAGGCA
TAAACTCAACATTTTGCCAACATAGGTTATAAAAAAACGTAGAGGTAAT
T GTGGCTAGAGTAACAAAGACTACAAAACCTTGGGCATGGGCTTGTTAC
TT TGAAATTCATCGACGCTAAGGGGTCTTGCCGCCGTGGGTTCGGTTTG
TAT
5167950 5167900 5167850 5167800
all4312two-component system5167767 -gt 5166997
Thats more like it. Now a person attuned to such
things can recognize the elements of a binding
site for the transcriptional regulator NtcA,
followed by the -10 region of a promoter,
properly spaced. The gene comes shortly after
that, now in the direct (blue) orientation. To
get back to the full sequence, click on Block and
then unInvert.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
12
Anabaena Chromosome (6413771 bp) 5167950-5967751
(inverted)
.............................................
AACTATAACAAAAATTTAATAATATTATCAACTTCGCTCTGGACAAGGCA
TAAACTCAACATTTTGCCAACATAGGTTATAAAAAAACGTAGAGGTAAT
T GTGGCTAGAGTAACAAAGACTACAAAACCTTGGGCATGGGCTTGTTAC
TT TGAAATTCATCGACGCTAAGGGGTCTTGCCGCCGTGGGTTCGGTTTG
TAT
5167950 5167900 5167850 5167800
all4312two-component system5167767 -gt 5166997
Thats more like it. Now a person attuned to such
things can recognize the elements of a binding
site for the transcriptional regulator NtcA,
followed by the -10 region of a promoter,
properly spaced. The gene comes shortly after
that, now in the direct (blue) orientation. To
get back to the full sequence, click on Block and
then unInvert.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
13
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
If suspicious, we could have found this same site
by a direct search for its consensus sequence
(though there are better ways than this),
clicking on Find, then Sequence, and typing in
the NtcA/promoter consensus sequence.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
14
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
If suspicious, we could have found this same site
by a direct search for its consensus sequence
(though there are better ways than this),
clicking on Find, then Sequence, and typing in
the NtcA/promoter consensus sequence.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
15
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
The NtcA binding sequence is flexible, like most
sequences of biological interest. Search tools
need to be similarly flexible.This search string
says Look for GTA followed by 8 nucleotides of
any sort, followed by TAC followed by 20 to 24
nucleotides, followed by TA, three nucleotides,
then a final T. Press Enter to find a matching
sequence.
Gene name Description Sequence
Sequence

GTA.8TAC.20,24TA...T
Contig GoTo Block Find Display
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16
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
It is sometimes easier to see patterns in DNA
sequences if we can engage our visual recognition
abilities. Click Display and then Base Symbols to
try it out for yourself.
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17
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCACGGCGGCAAGACCCCTTA
GCGTCGATGAATTTCA AAGTAACAAGCCCATGCCCAAGGTTTTGTAGTC
TTTGTTACTCTAGCCAC AATTACCTCTACGTTTTTTTATAACCTATGTT
GGCAAAATGTTGAGTTTA TGCCTTGTCCAGAGCGAAGTTGATAATATTA
TTAAATTTTTGTTATAGTT
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
It is sometimes easier to see patterns in DNA
sequences if we can engage our visual recognition
abilities. Click Display and then Base Symbols to
try it out for yourself.
Contig GoTo Block Find Display
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18
Anabaena Chromosome (6413771 bp) 5166951-5967950
.............................................
?????????????????CTAC
ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTG
T TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTT
AA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGG
GGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGG
TACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGA
TCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTA
AATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGC
GTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGC
AGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAAC
TCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCA
ACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAAT
TAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCA
CCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCA
AAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGGTA
TTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGATTC
CCCTCAACGATTTCA ATACAAACCGAACCCAC??????
???????? ?????????????????
????? ??????????
??????????? ????????????????
???????
5166961 5167001 5167051 5167101 5167151 5167201 51
67251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851 5167901
all4312two-component system5166997 lt- 5167767
Purines are represented as open symbols and
pyrimidines as filled in symbols. A and T are
purple, G and C are green. Fortunately, you dont
have to remember any of this to recognize
patterns. Look at the top line. Its immediately
evident (as it probably was not before) that
all4312 is followed by a string of... pyrimidines
and then a string of purines. Possibly a
termination region? Lets look beyond. Press the
right arrow key to move the display one line down.
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19
Anabaena Chromosome (6413771 bp) 5166901-5967950
.............................................
AACCAAGCCGATGAAGAATGGAACTAA???
?????????????????CT
AC ACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTT
TGT TAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATG
TTAA ATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGC
GGGGA TCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAAT
GGTACG CGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCT
GATCGGC TCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAAC
TAAATTCC TGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACG
GCGTTGGAC TAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGA
GCAGTAGGTG TGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAA
ACTCCTGCATC CCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTT
CAACCCGGCAAC GATATCAGCCTCATTAGTCCGAGCAGATAACATGAGA
ATTAGCGGCTGTT GCTGACGATGCAGCCAACGGCAAAATTCAATACCGT
CACCATCTGGCAAA TCAGCATCCAGAATCACTAGAGTTGGCTGATGGCT
CAAAAAGGCTTCCCT TGCTTGATATATGCTGGCGGCTTGATGCACACGG
TATTCCAATTGTTGCA AGTGCCAACCCAGCAACGACCTCAGATGGGGAT
TCCCCTCAACGATTTCA ATACAAACCGAACCCAC?????
???? ?????????????????
????? ??????????
???????????
5166901 5166961 5167001 5167051 5167101 5167151 51
67201 5167251 5167301 5167351 5167401 5167451
5167501 5167551 5167601 5167651 5167701 5167751
5167801 5167851
alr4311ABC transporter5166172 -gt
5166927 all4312two-component system5166997 lt-
5167767
From the change in color from yellow to blue,
weve evidently run into a gene on the other
strand, this one also ending in a string of
pyrimidines. Lets look further by clicking on
PgUp.
Contig GoTo Block Find Display
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20
Anabaena Chromosome (6413771 bp) 5165951-5966950
.............................................
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAAC
CGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAAT
T GATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA????
?? ???????
ATGACAGCCCAATTAAGGCTAGAAC
AAGT TAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAAT
ATTGC AGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATT
ATTGGC CCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACC
GCCTCAG TGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATA
TCCGCAAA TTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTA
CAAGAGCCA AAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACC
CTTTAATTTT GCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAG
TCATTGGGCGG AACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACT
GAGGTACAACTT TCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTG
CTTTAGTCATTCA ACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCA
TCTAGATATTGGTA TAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTA
ACTCAAACTCATCAC ACAACAATTGTGATGGTAAACAGCCAGCTAGACT
TCACTCAGATGTTTTG TAATCGGCTTTTGTATTTACAGCAAGGACGTTT
ATTGGTTAATCAAACAG CTTCTAACATCGACTGGATTGACTTACAAAAA
AGGTTGATGCACGCCGAA AACCAAGCCGATGAAGAATGGAACTAA?
??
5165961 5166001 5166051 5166101 5166151 5166201 51
66251 5166301 5166351 5166401 5166451
5166501 5166551 5166601 5166651 5166701 5166751
5166801 5166851 5166901
alr4310hypothetical protein5165532 -gt
5166086 alr4311ABC transporter5166172 -gt
5166927
The intergenic region between alr4310 and alr4311
shows a remarkable pattern. Ill give you a few
seconds to try to find it yourself...
The intergenic region between alr4310 and alr4311
shows a remarkable pattern. Ill give you a few
seconds to try to find it yourself......a series
of tandem repeats. Now that we see it by eye, we
can ask the computer to find them in a more
systematic fashion. Click on Display and then
Tandem repeats.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
21
Anabaena Chromosome (6413771 bp) 5165951-5966950
.............................................
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAAC
CGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAAT
T GATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA????
?? ???????
ATGACAGCCCAATTAAGGCTAGAAC
AAGT TAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAAT
ATTGC AGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATT
ATTGGC CCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACC
GCCTCAG TGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATA
TCCGCAAA TTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTA
CAAGAGCCA AAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACC
CTTTAATTTT GCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAG
TCATTGGGCGG AACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACT
GAGGTACAACTT TCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTG
CTTTAGTCATTCA ACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCA
TCTAGATATTGGTA TAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTA
ACTCAAACTCATCAC ACAACAATTGTGATGGTAAACAGCCAGCTAGACT
TCACTCAGATGTTTTG TAATCGGCTTTTGTATTTACAGCAAGGACGTTT
ATTGGTTAATCAAACAG CTTCTAACATCGACTGGATTGACTTACAAAAA
AGGTTGATGCACGCCGAA AACCAAGCCGATGAAGAATGGAACTAA?
??
5165961 5166001 5166051 5166101 5166151 5166201 51
66251 5166301 5166351 5166401 5166451
5166501 5166551 5166601 5166651 5166701 5166751
5166801 5166851 5166901
alr4310hypothetical protein5165532 -gt
5166086 alr4311ABC transporter5166172 -gt
5166927
The intergenic region between alr4310 and alr4311
show a remarkable pattern. Ill give you a few
seconds to try to find it yourself......a series
of tandem repeats. Now that we see it by eye, we
can ask the computer to find them in a more
systematic fashion. Click on Display and then
Tandem repeats.
Alternate starts Annotated features Local
features Tandem repeats Inverted repeats Base
symbols
Tandem repeats
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
22
Anabaena Chromosome (6413771 bp) 5165951-5966950
.............................................
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAAC
CGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAAT
T GATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA????
?? ???????
ATGACAGCCCAATTAAGGCTAGAAC
AAGT TAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAAT
ATTGC AGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATT
ATTGGC CCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACC
GCCTCAG TGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATA
TCCGCAAA TTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTA
CAAGAGCCA AAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACC
CTTTAATTTT GCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAG
TCATTGGGCGG AACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACT
GAGGTACAACTT TCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTG
CTTTAGTCATTCA ACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCA
TCTAGATATTGGTA TAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTA
ACTCAAACTCATCAC ACAACAATTGTGATGGTAAACAGCCAGCTAGACT
TCACTCAGATGTTTTG TAATCGGCTTTTGTATTTACAGCAAGGACGTTT
ATTGGTTAATCAAACAG CTTCTAACATCGACTGGATTGACTTACAAAAA
AGGTTGATGCACGCCGAA AACCAAGCCGATGAAGAATGGAACTAA?
??
5165961 5166001 5166051 5166101 5166151 5166201 51
66251 5166301 5166351 5166401 5166451
5166501 5166551 5166601 5166651 5166701 5166751
5166801 5166851 5166901
alr4310hypothetical protein5165532 -gt
5166086 alr4311ABC transporter5166172 -gt
5166927
The machine saw more than we did! Not only are
the repeats we saw more extensive, but there is
also another set of repeats nearby. What do they
mean? Hard to say, but certainly our chances of
figuring them out are better if we can engage our
visual imagination and if we can see them in a
biological context.
Contig GoTo Block Find Display
PgUp/PgDn Help Quit
End
23
Scenario 6
Analysis Tools for directly examining
sequenceSummary

• (article of faith) The freshest insights and
  most fundamental discoveries require intimate
  contact with the basic phenomenon.
• In genomic analysis, the basic phenomenon is
  often the genome.
• The sequence interface makes it possible to view
  DNA features within a biological context.
• The interface provides tool to aid discovery of
  features within noncoding DNA.

Software that does most of what you saw already
exists, but it would need to be rewritten before
it could serve as a web interface.