Lives of the Scientist

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Lives of the Scientist
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Genetic Basis of Differentiation
Events in time and space . . .
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Genetic Basis of Differentiation
Events in time and space . . .
. . . driven by patterned gene expression
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Genetic Basis of Differentiation
Events in time and space . . .
. . . driven by patterned gene expression
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Genetic Basis of Differentiation
Events in time and space . . .
. . . driven by patterned gene expression
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Genetic Basis of Differentiation
How?
Environmental Signal
Developmental Response
NH3
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Genetic Basis of Differentiation
How?
Developmental Response
Environmental Signal
NH3
Histidine Kinase
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Genetic Basis of Differentiation
How?
Developmental Response
Environmental Signal
NH3
histidine
Histidine Kinase
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Genetic Basis of Differentiation
How?
Developmental Response
Environmental Signal
NH3
Histidine Kinase
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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

Genetic Basis of Differentiation
How?
Developmental Response
Environmental Signal
NH3
Histidine Kinase
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Genes Functionally Related to His Kinase
Find similar genes
. . . (13 total)
Blast
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MWHIQDSIITLSNHNQYLTFYKNQVKNPERFCRNVNQFDSQIDFVSCDIL
ELKDGRFFEQYSKPLRLAEEIIGTVWSFRDITESQQAKEENRRIIQQE
KQ LAEDRAYFTSMIFHEFRNPLNIISYSTSLLKRHSHHWSEEKKLQCL
QNLQ TAVEQINQFTDEVLIIESVEAGKLQYELKPIDLNLFCREVLAEM
SLYTKG ASQFLLFQNK
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A new family of proteins?!A type of transposase?
...ATTTCTCTAGAAAGGCTGAAGGGGGGACAAGCACCCGAAAGCCTTTG
TGCT......TAAAGAGATCTTTCCGACTTCCCCCCTGTTCGTGGGCTT
TCGGAAACACGA...
...ATACAGTCAGCTTTATAGGCTTCATGTCGCCCCTTCAGCTAGAAAGG
TACATA......TATGTCAGTCGAAATATCCGAAGTACAGCGGGGAAGT
CGATCTTTCCATGTAT...
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A new family of proteins?!A type of transposase?
...ATTTCTCTAGAAAGGCTGAAGGGGGGACAAGCACCCGAAAGCCTTTG
TGCT......TAAAGAGATCTTTCCGACTTCCCCCCTGTTCGTGGGCTT
TCGGAAACACGA...
...ATACAGTCAGCTTTATAGGCTTCATGTCGCCCCTTCAGCTAGAAAGG
TACATA......TATGTCAGTCGAAATATCCGAAGTACAGCGGGGAAGT
CGATCTTTCCATGTAT...
38
A new family of proteins?!A type of transposase?
...ATTTCTCTAGAAAGGCTGAAGGGGGGACAAGCACCCGAAAGCCTTTG
TGCT......TAAAGAGATCTTTCCGACTTCCCCCCTGTTCGTGGGCTT
TCGGAAACACGA...
...ATACAGTCAGCTTTATAGGCTTCATGTCGCCCCTTCAGCTAGAAAGG
TACATA......TATGTCAGTCGAAATATCCGAAGTACAGCGGGGAAGT
CGATCTTTCCATGTAT...
39
A new family of proteins?!A type of transposase?
Is Npr3008 a transposase?
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Observation
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation
Photos courtesy of www.webshots.com and Peter
Smallwood
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Observation
Photos courtesy of www.webshots.com and Peter
Smallwood
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Filters Information reducersSquirrel filter
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Filters Information reducersMolecular filter
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Filters Information reducersSequence filter
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How do Biologists use Bioinformation?
Gene finder
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How do Biologists use Bioinformation?
Gene finder
Interpolated Markov model
Conform to standard model
Challenge accepted beliefs
Predicted genes
Candidate genes
Predicted genes
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How do Biologists use Bioinformation?
Gene finder
Interpolated Markov model
Conform to standard model
Predicted genes
Candidate genes
Predicted genes
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How do Biologists use Bioinformation?
Gene finder
Interpolated Markov model
Conform to standard model
Challenge accepted beliefs
Predicted genes
Candidate genes
Predicted genes
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Filters are powerful
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Filters Constrain New Discovery
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Filters are tempting
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Filters are tempting
Globin
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The Death of Science
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Current State of Affairs
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Current State of Affairs
1. Need high-level filters
2. Need access to raw phenomena
AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTT
TGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGA
CCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACC
TTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTT
CCTCTAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTT
CTGATTCAGTTTGGGTATTGCCTGTTTGAGTACCAAAAAATAAACCAATA
TTAGAC
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Current State of Affairs
1. Need high-level filters
2. Need access to raw phenomena
3. Need ability to build new tools
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We need
Biologists . . .
. . . and Programmers
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Current State of Affairs
1. Need high-level filters
2. Need access to raw phenomena
3. Need ability to build new tools
Need biologist programmers
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AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTT
TGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGA
CCTACAAATTTACCATCACGAACAGCTTTGARYGACTCACTGAATTCLAR
ATAACCTTCTGTAGGCCASONATAGCCAACTGTTTCACCACCATTTTCTG
AAATTTTTTCCTCT
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Why hasnt this happened?
Part of bioinformatic program written in C
if (pcInFile NULL) pfInFile stdin else
pfInFile fopen(pcInFile, "r")
pfOutFile fopen( pcOutFile, "w" ) if (
pfInFile NULL) fprintf( stderr, "ERROR
opening s\n", pcInFile ) exit(1)
if (pfOutFile NULL) fprintf( stderr, "ERROR
opening s\n", pcOutFile ) exit(1)
fputc( fgetc(pfInFile), pfOutFile ) / deal
with first '' in file / for ( )
if (processIdentifier( pfInFile, pfOutFile
)) else
break
if (processSequence( pfInFile, pfOutFile
)) else
break
fclose( pfInFile ) fclose( pfOutFile
)
83
Why hasnt this happened?
Part of bioinformatic program written in Perl
sub match_positions my pattern local
_ (pattern, _) _at__ my _at_results
local matchStart my instrumentedPattern
qr/(? matchStart pos() )pattern/
while (/instrumentedPattern/g)
my nextStart pos() push _at_results,
"matchStart..nextStart)" pos() matc
hStart1 return _at_results
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Why hasnt this happened?
Biologists will not come to programming
Programming must come to biologists
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BioLingua
86
Genetic Basis of Differentiation
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Genetic Basis of Differentiation
RR
HK
HK-upstream
HK-downstream
88
Genetic Basis of Differentiation
HK
RR
HK-upstream
HK-downstream
89
BioLingua
(GENES-DESCRIBED-BY "response regulator" IN Npun)

(Npun.NpF0304 Npun.NpR0355 Npun.NpR0450
Npun.NpF0484 Npun.NpR0589 Npun.NpF0832 N
pun.NpF0906 Npun.NpR0956 Npun.NpF1084 Npun
.NpF1085 Npun.NpR1109 Npun.NpF1184
Npun.NpF1278 Npun.NpR1450 Npun.NpF1453
Npun.NpF1516 Npun.NpR1633 Npun.NpR1678 N
pun.NpR1683 Npun.NpR1688 Npun.NpF1776 Npun
.NpR1779 Npun.NpF1800 Npun.NpR1903
Npun.NpR2091 Npun.NpF2162 Npun.NpR2263
Npun.NpF2346 Npun.NpF2364 Npun.NpR2420 N
pun.NpR2902 Npun.NpF2972 Npun.NpR3053 Npun
.NpF3084 Npun.NpR3197 Npun.NpR3241
Npun.NpF3659 Npun.NpF3676 Npun.NpR3733
Npun.NpF3829 Npun.NpR3907 Npun.NpR3959 N
pun.NpF3972 Npun.NpR4101 Npun.NpR4160 Npun
.NpR4165 Npun.NpF4214 Npun.NpR4435
Npun.NpF4460 Npun.NpR4503 Npun.NpR4743
Npun.NpR4768 Npun.NpF4909 Npun.NpR5015 N
pun.NpF5034 Npun.NpF5044 Npun.NpR5135 Npun
.NpR5136 Npun.NpR5316 Npun.NpF5361
Npun.NpF5636 Npun.NpF5682 Npun.NpF5759
Npun.NpF5763 Npun.NpF5788 Npun.NpR6014 N
pun.NpR6015 Npun.NpR6228 Npun.NpF6321 Npun
.NpR6360 Npun.NpF6363 Npun.pNpAF075
Npun.pNpBR039 Npun.pNpBF139 Npun.pNpBF146
Npun.pNpBR169 Npun.pNpBR170 Npun.pNpBF205
Npun.pNpEF003)
(GENE-UPSTREAM-OF NpF0304)

90
BioLingua
(GENE-UPSTREAM-OF NpF0304)

Npun.NpF0303

(GENES-UPSTREAM-OF (RESULT 1))
(Npun.NpF0303 Npun.NpF0356 Npun.NpF0451
Npun.NpF0483 Npun.NpR0590 Npun.NpF0831 N
pun.NpF0905 Npun.NpF0957 Npun.NpR1083 Npun
.NpF1084 Npun.NpR1110 Npun.NpF1183
Npun.NpF1277 Npun.NpR1451 Npun.NpR1452
Npun.NpR1515 Npun.NpF1634 Npun.NpR1679 N
pun.NpF1684 Npun.NpR1689 Npun.NpF1775 Npun
.NpF1780 Npun.NpF1799 Npun.NpR1904
Npun.NpR2092 Npun.NpF2161 Npun.NpR2264
Npun.NpR2345 Npun.NpF2363 Npun.NpR2421 N
pun.NpR2903 Npun.NpR2971 Npun.NpR3054 Npun
.NpR3083 Npun.NpR3198 Npun.NpF3242
Npun.NpR3658 Npun.NpF3675 Npun.NpR3734
Npun.NpR3828 Npun.NpF3908 Npun.NpR3960 N
pun.NpF3971 Npun.NpF4102 Npun.NpR4161 Npun
.NpF4166 Npun.NpR4213 Npun.NpR4436
Npun.NpF4459 Npun.NpR4504 Npun.NpR4744
Npun.NpR4769 Npun.NpR4908 Npun.NpF5016 N
pun.NpF5033 Npun.NpF5043 Npun.NpR5136 Npun
.NpF5137 Npun.NpF5317 Npun.NpF5360
Npun.NpR5635 Npun.NpF5681 Npun.NpF5758
Npun.NpR5762 Npun.NpR5787 Npun.NpR6015 N
pun.NpR6016 Npun.NpR6229 Npun.NpR6320 Npun
.NpF6361 Npun.NpF6362 Npun.pNpAF074
Npun.pNpBR040 Npun.pNpBF138 Npun.pNpBF145
Npun.pNpBR170 Npun.pNpBR171 Npun.pNpBR204
Npun.pNpER002)
(DESCRIPTIONS-OF )

91
BioLingua
DESCRIPTIONS-OF )

("two-component sensor histidine kinase
Nostoc sp. PCC 7120 gi25531611pirAD2200
two- "unknown protein Nostoc sp. PCC 7120 gi2
5534386pirAH1981 hypothetical protein alr1403
"tmRNA-binding protein Nostoc sp. PCC 7120 gi
22096164spQ8YM70SSRP_ANASP SsrA-binding
protein "GTP-binding protein era homolog" "unk
nown protein Nostoc sp. PCC 7120
gi25533156pirAF2229 hypothetical protein
asr3389 "ORF_IDtlr0160similar to ferredoxin
Thermosynechococcus elongatus BP-1
"hypothetical protein Nostoc sp. PCC 7120
gi25367067pirAH2295 hypothetical protein
alr3919 "two-component hybrid sensor and regulat
or Nostoc sp. PCC 7120 gi25532444pirAE2276
two- "hypothetical protein Nostoc sp. PCC 7120
gi25358966pirAG2158 hypothetical protein
alr2822 "two-component response regulator Nosto
c sp. PCC 7120 gi25533086pirAF2158
two-component "probable two-component sensor his
tidine kinase Gloeobacter violaceus
gi35214672dbjBAC92039.1 "phytochrome-like pr
otein Tolypothrix sp. PCC 7601"
"two-component sensor histidine kinase Nostoc
sp. PCC 7120 gi25530471pirAC1860
two-component NIL NIL NIL "hypothetical protei
n Nostoc sp. PCC 7120 gi25535333pirAI2179
hypothetical protein all2992 NIL "unknown prot
ein Nostoc sp. PCC 7120 gi25535440pirAI2275
hypothetical protein alr3760 "transcriptional re
gulator Nostoc sp. PCC 7120 gi25302898pirAB2
544 transcription regulator "similar to two-comp
onent sensor histidine kinase Nostoc sp. PCC
7120 gi25531791pirAD2385 "putative gluconol
actonase precursor Sinorhizobium meliloti
gi25369832pirG95274 probable
"similar to two-component sensor histidine
kinase Nostoc sp. PCC 7120 gi25531791pirAD23
85 "hypothetical protein Nostoc sp. PCC 7120 g
i25530521pirAC1903 hypothetical protein
asr0773 . . .
92
BioLingua
(DEFINE RR-class AS (GENES-DESCRIBED-BY
"response regulator" IN Npun) DISPLAY off)

"List of length 79 suppressed"
(DEFINE HK-class AS (GENES-DESCRIBED-BY
histidine kinase" IN Npun) DISPLAY off)

"List of length 89 suppressed"
(DEFINE HK-upstream AS (GENES-UPSTREAM-OF
HK-class) DISPLAY off)

"List of length 89 suppressed"
(DEFINE HK-downstream AS (GENES-DOWNSTREAM-OF
HK-class) DISPLAY off)

"List of length 89 suppressed"
(DEFINE HK-adjacent AS (UNION-OF
(HK-upstream HK-downstream)) DISPLAY off)

"List of length 178 suppressed"
(INTERSECTION-OF (HK-adjacent RR-class))

93
BioLingua
(INTERSECTION-OF (HK-adjacent RR-class))

22 elements in INTERSECTION (Npun.pNpBF2
05 Npun.pNpBF139 Npun.NpR6228 Npun.NpR5316
Npun.NpF4214 Npun.NpF3676 Npun.NpF3084
Npun.NpR3053 Npun.NpR1779 Npun.NpR0589
Npun.NpF0304 Npun.NpR1109 Npun.NpF1278
Npun.NpF1776 Npun.NpF1800 Npun.NpR2420
Npun.NpR2902 Npun.NpR3197 Npun.NpR4503
Npun.NpF5763 Npun.NpF6363 Npun.pNpBF146)
(DEFINE RR-candidates AS (SET-DIFFERENCE RR-class
(RESULT 10)) DISPLAY off)

"List of length 57 suppressed"

94
Genes Functionally Related to His Kinase
Find similar genes
. . . (13 total)
95
BioLingua
(INTERSECTION-OF (RR-adjacent HK-class))

24 elements in INTERSECTION (Npun.pNpBF2
05 Npun.pNpBF139 Npun.NpR6228 Npun.NpR5316
Npun.NpF4214 Npun.NpF3676 Npun.NpF3084
Npun.NpR3053 Npun.NpR1779 Npun.NpR0589
Npun.NpF0304 Npun.NpR1109 Npun.NpF1278
Npun.NpF1776 Npun.NpF1800 Npun.NpR2420
Npun.NpR2902 Npun.NpR3197 Npun.NpR4503
Npun.NpF5763 Npun.NpF6363 Npun.pNpBF146)
(DEFINE RR-candidates AS (SET-DIFFERENCE RR-class
(RESULT 10)) DISPLAY off)

"List of length 57 suppressed"
(CONTEXT-OF NpF0304)

( sub) 523 (- Npun.NpF0303 two-component
sensor histidine) 85 (- Npun.NpF0304
two-component response regulat) 473 (-
Npun.NpF0305 hypothetical protein glr0895 ) 85
() (Npun.NpR0302 Npun.NpF0303 Npun.NpF030
4 Npun.NpF0305 Npun.NpR0306)
(ALL-ORTHOLOGS-OF )

96
BioLingua
(CONTEXT-OF NpF0304)

( sub) 523 (- Npun.NpF0303 two-component
sensor histidine) 85 (- Npun.NpF0304
two-component response regulat) 473 (-
Npun.NpF0305 hypothetical protein glr0895 ) 85
() (Npun.NpR0302 Npun.NpF0303 Npun.NpF030
4 Npun.NpF0305 Npun.NpR0306)
(ALL-ORTHOLOGS-OF )

((S7942.sef0159 Npun.NpR0302 Gvi.glr0573
A29413.Av?3368 A7120.all3154)
(S6803.sll1590 Npun.NpF0303 Gvi.gll0572
A29413.Av?1247 A7120.alr3155)
(S6803.sll1592 P9313.PMT1405 Npun.NpF0304
Gvi.gll0571 A29413.Av?1248 A7120.alr3156)
(Tery.Te?7017 Npun.NpF0305 Cwat.Cw?3050)
(Tery.Te?2243 TeBP1.tll0415 S6803.sll0270
S8102.SynW1782 S7942.sef1895
PRO1375.Pro0497 P9313.PMT1271 PMED4.PMM0497
Npun.NpR0306 Gvi.gll0025 Cwat.Cw?3016
A29413.Av?5206 A7120.all4248))

97
A new family of proteins?!A type of transposase?
Is Npr3008 a transposase?
98
BioLingua
(DEFINE extended-NpR3008 AS (SEQUENCE-OF
NpR3008 FROM -700 TO-END 700) DISPLAY off)

Results suppressed"
(BLAST extended-NpR3008 Npun)

Query Q-Start Q-End Subject
S-Start S-End E-value ID
1. "Seq 1" 1 2258 Npun.chromosome
3706846 3704589 0.0 100.0
2. "Seq 1" 293 1511 Npun.chromosome
4008429 4009647 0.0 100.0
3. "Seq 1" 293 1512 Npun.chromosome
7932036 7930817 0.0 99.92
4. "Seq 1" 293 1510 Npun.chromosome
4228111 4229328 0.0 99.92
5. "Seq 1" 293 1510 Npun.chromosome
3971285 3972502 0.0 99.92
6. "Seq 1" 293 1510 Npun.chromosome
4027833 4029050 0.0 99.75
7. "Seq 1" 293 1511 Npun.chromosome
2121987 2123204 0.0 99.67
8. "Seq 1" 293 1510 Npun.chromosome
2136737 2135521 0.0 99.67
9. "Seq 1" 397 1510 Npun.chromosome
2030748 2031861 0.0 99.64
10. "Seq 1" 1537 2258 Npun.pNpB
42015 42737 4.6d-83 80.5
11. "Seq 1" 1331 1420 Npun.chromosome
8036134 8036045 1.8d-8 83.33
12. "Seq 1" 1319 1385 Npun.chromosome
5915424 5915358 2.7d-4 83.58
13. "Seq 1" 1319 1385 Npun.chromosome
2577387 2577453 2.7d-4 83.58
(Temp27 Temp28 Temp29 Temp30 Temp31
Temp32 Temp33 Temp34 Temp35 Temp36 T
emp37 Temp38 Temp39)

99
BioLingua
(DEFINE extended-NpR3008 AS (SEQUENCE-OF
NpR3008 FROM -700 TO-END 700) DISPLAY off)

Results suppressed"
(BLAST extended-NpR3008 Npun)

Query Q-Start Q-End Subject
S-Start S-End E-value ID
1. "Seq 1" 1 2258 Npun.chromosome
3706846 3704589 0.0 100.0
2. "Seq 1" 293 1511 Npun.chromosome
4008429 4009647 0.0 100.0 . . .

(FOR-EACH hit IN
AS (subj S-start)
(GET-ELEMENTS (subject Subject-start) FROM hit)
AS start (- S-start 15)
AS end ( S-start 40)
AS left-end (SEQUENCE-OF subj FROM start
TO end)
COLLECT left-end)
100
BioLingua
(DEFINE extended-NpR3008 AS (SEQUENCE-OF
NpR3008 FROM -700 TO-END 700) DISPLAY off)

Results suppressed"
(BLAST extended-NpR3008 Npun)

Query Q-Start Q-End Subject
S-Start S-End E-value ID
1. "Seq 1" 1 2258 Npun.chromosome
3706846 3704589 0.0 100.0
2. "Seq 1" 293 1511 Npun.chromosome
4008429 4009647 0.0 100.0 . . .

(FOR-EACH hit IN
AS (subj S-start)
(GET-ELEMENTS (subject Subject-start) FROM hit)
AS start (- S-start 15)
AS end ( S-start 40)
AS left-end (SEQUENCE-OF subj FROM start
TO end)
COLLECT left-end)
("TACGCTCTATCTTCAGCAAGTTGTTTTTCTTGCTGTATAAT
TCGGCGATTCTCTTC" "AAAGAAACGCTAGAGGGGTGCATCCCAGTT
TTTATTATTCCAAAACAAATAAATAA" "AAACTGGGATGCACCCCTT
ATTAATGCTCTTTGGAGTCAATACTAATTTTGCCAAA"
"TACCTTTGTGATAGGGGGTGCATCCCAGTTTTTATTATTCCAAAACAA
ATAAATAA" "AAATTAGTTTATTATGGGTGCATCCCAGTTTTTATTA
TTCCAAAACAAATAAATAA" "CACCGATTCACTAATGGGTGCATCCC
AGTTTTTATTATTCCAAAACAAATAAATAA"
"ACTATTGTAGAGACTGGGTGCATCCCAGTTTTTATTATTCCAAAACAA
ATAAATAA" . . .
101
BioLingua
(ALIGNMENT-OF LINE-LENGTH 60 SEGMENT-LENGTH 60)

Seq 4 1 TACCTTTGT-GATAGGGGGTGCATCCCAG
TTTTTATTAT--TCCAAAACAAATAAATAA---------------
Seq 7 1 -ACTATTGTAGAGACTGGGTGCATCCCAGTTTTT
ATTAT--TCCAAAACAAATAAATAA---------------
Seq 2 1 -AAAGAAACGCTAGAGGGGTGCATCCCAGTTTTT
ATTAT--TCCAAAACAAATAAATAA---------------
Seq 5 1 AAATTAGTTTATTA-TGGGTGCATCCCAGTTTTT
ATTAT--TCCAAAACAAATAAATAA---------------
Seq 6 1 -CACCGATTCACTAATGGGTGCATCCCAGTTTTT
ATTAT--TCCAAAACAAATAAATAA---------------
Seq 8 1 ----------AAACTGGGATGCA-CCCAGTCTCT
ACAATAGTTCTAGA-GAACACATAACGTAAATAC------
Seq 3 1 ----------AAACTGGGATGCACCCC--TTATT
AATGCTCTTTGGAGTCAATAC-TAATTTTGCCAAA-----
Seq 9 1 -----------CATTGTCGCCCCTTGAAGTCATC
AAGAC-----TAGGTGTATCAATGACTCCTGAAGAAGA--
Seq 12 1 ------------------GTTCAGCTTGGTAATA
GCTGTAGTTAATAATGCGAGAGCGATGTTTTTCGAGATAA
Seq 1 1 ---------TACGCTCTATCTTCAGCAAGTTGTT
TTTCT--TGCTGTATAATTCGGCGATTCTCTTC-------
Seq 10 1 --------------GGTCGGGAAATTGCGAGATT
ATTCAGTGGCGAAGTAGTGGGAGAACTACCATTGAT----
Seq 11 1 ------------TTGAACAAATTTGTTCGTGGAA
ATGGTAATTGGAAATTTGCTGCGGAATGCGGTGA------
Seq 13 1 ------------ATTATTAACTACAGCTATTACC
AAGCTGAACAACTGTGTTCTATTGGTTCTGGTTC------
consensus 1
102
Genetic Basis of Differentiation
Anabaena
Not Synechocystis, Trichodesmium,
103
BioLingua
(DEFINE diff-cb AS (Npun Avar A7120) DISPLAY off)

"List of length 3 suppressed"
(DEFINE non-diff-cb AS (REMOVE-FROM-SET
loaded-organisms diff-cb) DISPLAY off)

"List of length 10 suppressed"
(DEFINE diff-cb-specific AS
(COMMON-ORTHOLOGS-OF diff-cb NOT-IN non-diff-cb)
DISPLAY off)

"List of length 661 suppressed"
104
BioLingua

• Provides knowledge in accessible form

• Provides tools accessed in common way

• Provides results that can be manipulated

• Provides a programming language that speaks
  to biologists

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Credits
West Coast - Jeff Shrager - JP Massar - Mike T
ravers
VCU - Austin Hess - James Mastros - Sarah Cous
ins - Yue Zhao
BioLingua http//ramsites.net/biolingua/help
Jeff Elhai Center for the Study of Biological
Complexity Virginia
Commonwealth University
Phone [phone]
E-mail ElhaiJ_at_VCU.Edu