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 begin:1. Click on Slide Show, (on the upper toolbar)2. Click View Show3. Click Continue button
Continue
Scenario 6
You’re intrigued by the motif you found in front of Anabaena PCC 7120 all4312 and its cyanobacterial orthologs (see Scenarios 1 and 5).
You’d like to look more deeply into it, by examining the sequence near the orf. You’re not sure what you’re looking for, and you’re open for anything.
Continue
Scenario 6
Analysis: Tools for directly examining sequence
Anab7120:all4312
NostPunc:618.077
TricEryt:5.6053
Syny6803:sll1330
TherElon:tlr1330
Anabaena PCC 7120: all4312OptionsAnnotateMain Menu History
Replicon: Chromosome
Coordinates: 5166997 (stop) <- 5167767 (start-GTG) System Length = 256 amino acids
Strand: Complementary
Function: Two-component response regulator System Syny6803:sll1330: Expression data (click to expand) Experiment
Mutant: None Syny6803:sll1330: Failed to segregate Experiment
Cyanobacterial orthologs: NostPunc TricEryt Syny6803 TherElon
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.
ALawrence/Collier conserved motif set
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
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.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
We want to display the motif predicted by Lawrence/Collier, so
click on Predicted features.
Alternate startsAnnotated featuresPredicted featuresPrivate featuresTandem repeatsInverted repeatsBase symbolsInvert display
Predicted features
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
I was hoping to see sequences I
recognized, but that’s made more difficult by the orf being on the wrong strand. I
could invert the entire display, but
instead I’ll just work on a segment. Click
Block.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
The highlighted orf sequence could now be
downloaded or first translated then downloaded, but I’m interested now only in the region preceding the gene. Click Define, in order to highlight a new block of
sequence.DefineInvert
TranslateSaveTools
Define
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
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).
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
Now that the bottom four lines are blocked, Click on
Block and then Invert.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
Now that the bottom four lines are blocked, Click on
Block and then Invert.
DefineInvert
TranslateSaveTools
Invert
AACTATAACAAAAATTTAATAATATTATCAACTTCGCTCTGGACAAGGCATAAACTCAACATTTTGCCAACATAGGTTATAAAAAAACGTAGAGGTAATTGTGGCTAGAGTAACAAAGACTACAAAACCTTGGGCATGGGCTTGTTACTTTGAAATTCATCGACGCTAAGGGGTCTTGCCGCCGTGGGTTCGGTTTGTAT
all4312two-component system
5167767 -> 5166997
Anabaena Chromosome (6413771 bp): 5167950-5967751 (inverted)
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5167950516790051678505167800
That’s 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.
AACTATAACAAAAATTTAATAATATTATCAACTTCGCTCTGGACAAGGCATAAACTCAACATTTTGCCAACATAGGTTATAAAAAAACGTAGAGGTAATTGTGGCTAGAGTAACAAAGACTACAAAACCTTGGGCATGGGCTTGTTACTTTGAAATTCATCGACGCTAAGGGGTCTTGCCGCCGTGGGTTCGGTTTGTAT
all4312two-component system
5167767 -> 5166997
Anabaena Chromosome (6413771 bp): 5167950-5967751 (inverted)
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5167950516790051678505167800
That’s 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.
InvertTranslate
SaveTools
unInvert
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
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.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901 Gene name
DescriptionSequenceSequence
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.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901 Gene name
DescriptionSequenceSequence GTA.{8}TAC.{20,24}TA...T
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.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
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.
GCTGAGTTAGGAGTAAAAATCATTATTTTTCCTCCCTCTGCCTCCTCTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCACGGCGGCAAGACCCCTTAGCGTCGATGAATTTCAAAGTAACAAGCCCATGCCCAAGGTTTTGTAGTCTTTGTTACTCTAGCCACAATTACCTCTACGTTTTTTTATAACCTATGTTGGCAAAATGTTGAGTTTATGCCTTGTCCAGAGCGAAGTTGATAATATTATTAAATTTTTGTTATAGTT
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
Alternate startsAnnotated
featuresLocal features
Tandem repeatsInverted repeatsBase symbolsBase symbols
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.
□■■□□□■■□□□□□■□□□□□■■□■■□■■■■■■■■■■■■■■□■■■■■■CTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCAC□□■□□■■■□■■■■■■■□□■□■■□□■□□□■■■■□□□□■□□■□□□■■■□■□■■■□□□□■■■■□■□□■■■■■□■■□■■■■□□■■□■□□■■□■■■■■□■□■■■■■■■□■□□■■■□■□■■□□■□□□□■□■■□□□■■■□■□■■■■□■■■□□□□■□□□□■■□□■□□■□■■□■■□□□■■■■■□■■□■□□■■
5166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 516780151678515167901
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166951-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
Purines are represented as open symbols and pyrimidines as filled in symbols. A and T are purple, G
and C are green. Fortunately, you don’t have to remember any of this to recognize patterns. Look at the top line. It’s 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? Let’s look beyond. Press the right arrow key to move the display one line down.
AACCAAGCCGATGAAGAATGGAACTAA□■■■■■■■■■■■■■□■■■■■■□■ □■■□□□■■□□□□□■□□□□□■■□■■□■■■■■■■■■■■■■■□■■■■■■CTACACCCTCTGCCCACTTAGAGTTGAGCGTTGGTTGCTAAATCTTTCTTTTGTTAACTTTGCTTGTGTTTGTGGAGGATTAGCATTCAAAATTTCCATGTTAAATCGGTATCCAACATTGCGGATAGTCTGAATGAGGCTAGGTTGGCGGGGATCAAGTTCTACTTTTTTACGTAACGATAGAACATGAGTGTCAATGGTACGCGGATTGTCGATAGCGTCAGGCCACGCACGACGTAGCAACTCTGATCGGCTCAAAGGTACTCCACCAGCTTGCGCCAAAACGTACAACAAACTAAATTCCTGTGGAGTCAGGTCGATAAACTCCCCTTGGAATCGTACACGGCGTTGGACTAAATCGATTTGCAAAGTACCATAATCCAAATAAGCAGGAGCAGTAGGTGTGCGCTTGCGGCGGATTAATGCCTCTACCCTAGCCAAAAACTCCTGCATCCCAAATGGTTTGCTCAAGTAATCATCAGCTCCCGCCTTCAACCCGGCAACGATATCAGCCTCATTAGTCCGAGCAGATAACATGAGAATTAGCGGCTGTTGCTGACGATGCAGCCAACGGCAAAATTCAATACCGTCACCATCTGGCAAATCAGCATCCAGAATCACTAGAGTTGGCTGATGGCTCAAAAAGGCTTCCCTTGCTTGATATATGCTGGCGGCTTGATGCACACGGTATTCCAATTGTTGCAAGTGCCAACCCAGCAACGACCTCAGATGGGGATTCCCCTCAACGATTTCAATACAAACCGAACCCAC□□■□□■■■□■■■■■■■■□■□■■□■■□■■■■■■■□□□■□□■□□□■■■□■□■■■□□□□■■■■□■□□■■■■■□■■□■■■■□□■■□■□□■■□■■■■■□■□■■■■■■■□■□□■■■□■□■■□□■□□□□■□■■□□□■■■□
51669015166961516700151670515167101516715151672015167251 51673015167351 51674015167451 51675015167551 51676015167651 51677015167751 51678015167851
alr4311ABC transporter
5166172 -> 5166927
all4312two-component system
5166997 <- 5167767
Anabaena Chromosome (6413771 bp): 5166901-5967950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
From the change in color from yellow to blue, we’ve evidently run into a gene on the other strand, this one
also ending in a string of pyrimidines. Let’s look further by clicking on PgUp.
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAACCGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAATTGATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA□■■■■□□■■■■□□□□■■■■□□□■■■□□□■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ATGACAGCCCAATTAAGGCTAGAACAAGTTAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAATATTGCAGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATTATTGGCCCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACCGCCTCAGTGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATATCCGCAAATTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTACAAGAGCCAAAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACCCTTTAATTTTGCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAGTCATTGGGCGGAACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACTGAGGTACAACTTTCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTGCTTTAGTCATTCAACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCATCTAGATATTGGTATAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTAACTCAAACTCATCACACAACAATTGTGATGGTAAACAGCCAGCTAGACTTCACTCAGATGTTTTGTAATCGGCTTTTGTATTTACAGCAAGGACGTTTATTGGTTAATCAAACAGCTTCTAACATCGACTGGATTGACTTACAAAAAAGGTTGATGCACGCCGAAAACCAAGCCGATGAAGAATGGAACTAA□■■■■■■■■■■■■■□■■■■■■□■
5165961516600151660515166101516615151662015166251 51663015166351 51664015166451 51665015166551 51666015166651 51667015166751 516680151668515166901
alr4310hypothetical protein5165532 -> 5166086
alr4311ABC transporter
5166172 -> 5166927
Anabaena Chromosome (6413771 bp): 5165951-5966950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
The intergenic region between alr4310 and alr4311 shows a remarkable pattern. I’ll give you a few
seconds to try to find it yourself...
The intergenic region between alr4310 and alr4311 shows a remarkable pattern. I’ll 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.
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAACCGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAATTGATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA□■■■■□□■■■■□□□□■■■■□□□■■■□□□■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ATGACAGCCCAATTAAGGCTAGAACAAGTTAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAATATTGCAGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATTATTGGCCCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACCGCCTCAGTGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATATCCGCAAATTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTACAAGAGCCAAAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACCCTTTAATTTTGCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAGTCATTGGGCGGAACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACTGAGGTACAACTTTCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTGCTTTAGTCATTCAACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCATCTAGATATTGGTATAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTAACTCAAACTCATCACACAACAATTGTGATGGTAAACAGCCAGCTAGACTTCACTCAGATGTTTTGTAATCGGCTTTTGTATTTACAGCAAGGACGTTTATTGGTTAATCAAACAGCTTCTAACATCGACTGGATTGACTTACAAAAAAGGTTGATGCACGCCGAAAACCAAGCCGATGAAGAATGGAACTAA□■■■■■■■■■■■■■□■■■■■■□■
5165961516600151660515166101516615151662015166251 51663015166351 51664015166451 51665015166551 51666015166651 51667015166751 516680151668515166901
alr4310hypothetical protein5165532 -> 5166086
alr4311ABC transporter
5166172 -> 5166927
Anabaena Chromosome (6413771 bp): 5165951-5966950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
The intergenic region between alr4310 and alr4311 show a remarkable pattern. I’ll 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 startsAnnotated
featuresLocal features
Tandem repeatsInverted repeatsBase symbols
Tandem repeats
CCAAAGCAAAACAGGTATAGACACCACTGATGTTCGCCCTTTAGCGCAACCGTGGATGTATTTGATTTTATTAGGATTTACACTATTACTACTTTTAATTGATGCTTGGGCGATCGCCACAGCTATAGCCATCTAA□■■■■□□■■■■□□□□■■■■□□□■■■□□□■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ATGACAGCCCAATTAAGGCTAGAACAAGTTAATCTGTTTGCCAAGCTAAAAACCCAGCTTCAGGGCTACCCAATATTGCAGGATATCTCTTTTGAGATTAACTCTGGCGATCGCCTAGCAATTATTGGCCCCTCCGGTGCTGGTAAAACTTCTTTACTACGTCTAATTAACCGCCTCAGTGAACCTAATAGCGGCAAAATTTTTTTAGAAAATCAAGAATATCCGCAAATTCCTGTTATCCAGTTGCGCCAGATAGTGACCCTGGTATTACAAGAGCCAAAGTTTCTGGGGATGACAGTCCAACAAGCCTTAGCTTACCCTTTAATTTTGCGCGGTTTGACCAAAGAGACGATTCAGCAGCGAGTCAGTCATTGGGCGGAACAGCTGCAAATCCCTGGTGATTGGTTAGGACGCACTGAGGTACAACTTTCGGCTGGACAGAGACAGCTCGTAGCGATCGCTCGTGCTTTAGTCATTCAACCGAAAATCCTCCTGTTAGATGAGCCAACCTCTCATCTAGATATTGGTATAGCCTCCCATCTTATCCAAGTCTTAACCCAGCTAACTCAAACTCATCACACAACAATTGTGATGGTAAACAGCCAGCTAGACTTCACTCAGATGTTTTGTAATCGGCTTTTGTATTTACAGCAAGGACGTTTATTGGTTAATCAAACAGCTTCTAACATCGACTGGATTGACTTACAAAAAAGGTTGATGCACGCCGAAAACCAAGCCGATGAAGAATGGAACTAA□■■■■■■■■■■■■■□■■■■■■□■
5165961516600151660515166101516615151662015166251 51663015166351 51664015166451 51665015166551 51666015166651 51667015166751 516680151668515166901
alr4310hypothetical protein5165532 -> 5166086
alr4311ABC transporter
5166172 -> 5166927
Anabaena Chromosome (6413771 bp): 5165951-5966950
.........|.........|.........|.........|.........|
Contig GoTo Block Find Display PgUp/PgDn Help Quit
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.
End
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.
Scenario 6
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.
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