bio 1.4.0 → 1.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (82) hide show
  1. data/ChangeLog +1712 -0
  2. data/KNOWN_ISSUES.rdoc +11 -1
  3. data/README.rdoc +3 -2
  4. data/RELEASE_NOTES.rdoc +65 -127
  5. data/bioruby.gemspec +38 -2
  6. data/doc/RELEASE_NOTES-1.4.0.rdoc +167 -0
  7. data/doc/Tutorial.rd +74 -16
  8. data/doc/Tutorial.rd.html +68 -16
  9. data/lib/bio.rb +2 -0
  10. data/lib/bio/appl/clustalw/report.rb +18 -0
  11. data/lib/bio/appl/paml/codeml/report.rb +579 -21
  12. data/lib/bio/command.rb +149 -21
  13. data/lib/bio/db/aaindex.rb +11 -1
  14. data/lib/bio/db/embl/sptr.rb +1 -1
  15. data/lib/bio/db/fasta/defline.rb +7 -2
  16. data/lib/bio/db/fasta/qual.rb +24 -0
  17. data/lib/bio/db/fasta/qual_to_biosequence.rb +29 -0
  18. data/lib/bio/db/fastq.rb +15 -0
  19. data/lib/bio/db/go.rb +2 -2
  20. data/lib/bio/db/kegg/common.rb +109 -5
  21. data/lib/bio/db/kegg/genes.rb +61 -15
  22. data/lib/bio/db/kegg/genome.rb +43 -38
  23. data/lib/bio/db/kegg/module.rb +158 -0
  24. data/lib/bio/db/kegg/orthology.rb +40 -1
  25. data/lib/bio/db/kegg/pathway.rb +254 -0
  26. data/lib/bio/db/medline.rb +6 -2
  27. data/lib/bio/io/flatfile/autodetection.rb +6 -0
  28. data/lib/bio/location.rb +39 -0
  29. data/lib/bio/reference.rb +24 -0
  30. data/lib/bio/sequence.rb +2 -0
  31. data/lib/bio/sequence/adapter.rb +1 -0
  32. data/lib/bio/sequence/format.rb +14 -0
  33. data/lib/bio/sequence/sequence_masker.rb +95 -0
  34. data/lib/bio/tree.rb +4 -4
  35. data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +5 -0
  36. data/lib/bio/version.rb +1 -1
  37. data/setup.rb +5 -0
  38. data/test/data/KEGG/K02338.orthology +180 -52
  39. data/test/data/KEGG/M00118.module +44 -0
  40. data/test/data/KEGG/T00005.genome +140 -0
  41. data/test/data/KEGG/T00070.genome +34 -0
  42. data/test/data/KEGG/b0529.gene +47 -0
  43. data/test/data/KEGG/ec00072.pathway +23 -0
  44. data/test/data/KEGG/hsa00790.pathway +59 -0
  45. data/test/data/KEGG/ko00312.pathway +16 -0
  46. data/test/data/KEGG/map00030.pathway +37 -0
  47. data/test/data/KEGG/map00052.pathway +13 -0
  48. data/test/data/KEGG/rn00250.pathway +114 -0
  49. data/test/data/clustalw/example1.aln +58 -0
  50. data/test/data/go/selected_component.ontology +12 -0
  51. data/test/data/go/selected_gene_association.sgd +31 -0
  52. data/test/data/go/selected_wikipedia2go +13 -0
  53. data/test/data/medline/20146148_modified.medline +54 -0
  54. data/test/data/paml/codeml/models/aa.aln +26 -0
  55. data/test/data/paml/codeml/models/aa.dnd +13 -0
  56. data/test/data/paml/codeml/models/aa.ph +13 -0
  57. data/test/data/paml/codeml/models/alignment.phy +49 -0
  58. data/test/data/paml/codeml/models/results0-3.txt +312 -0
  59. data/test/data/paml/codeml/models/results7-8.txt +340 -0
  60. data/test/functional/bio/io/test_togows.rb +8 -8
  61. data/test/functional/bio/test_command.rb +7 -6
  62. data/test/unit/bio/appl/clustalw/test_report.rb +80 -0
  63. data/test/unit/bio/appl/paml/codeml/test_rates.rb +6 -6
  64. data/test/unit/bio/appl/paml/codeml/test_report.rb +231 -24
  65. data/test/unit/bio/appl/paml/codeml/test_report_single.rb +46 -0
  66. data/test/unit/bio/db/embl/test_sptr.rb +1 -1
  67. data/test/unit/bio/db/fasta/test_defline.rb +160 -0
  68. data/test/unit/bio/db/fasta/test_defline_misc.rb +490 -0
  69. data/test/unit/bio/db/kegg/test_genes.rb +281 -1
  70. data/test/unit/bio/db/kegg/test_genome.rb +408 -0
  71. data/test/unit/bio/db/kegg/test_module.rb +246 -0
  72. data/test/unit/bio/db/kegg/test_orthology.rb +95 -0
  73. data/test/unit/bio/db/kegg/test_pathway.rb +1250 -0
  74. data/test/unit/bio/db/test_aaindex.rb +8 -7
  75. data/test/unit/bio/db/test_fastq.rb +36 -0
  76. data/test/unit/bio/db/test_go.rb +171 -0
  77. data/test/unit/bio/db/test_medline.rb +148 -0
  78. data/test/unit/bio/db/test_qual.rb +9 -2
  79. data/test/unit/bio/sequence/test_sequence_masker.rb +169 -0
  80. data/test/unit/bio/test_tree.rb +260 -1
  81. data/test/unit/bio/util/test_contingency_table.rb +7 -7
  82. metadata +53 -6
data/lib/bio/tree.rb CHANGED
@@ -486,14 +486,14 @@ module Bio
486
486
  _clear_cache
487
487
  removed_rel = []
488
488
  @pathway.relations.delete_if do |rel|
489
- if yield rel.node[0], rel.node[1], edge then
489
+ if yield rel.node[0], rel.node[1], rel.edge then
490
490
  removed_rel << rel
491
491
  true
492
492
  end
493
493
  end
494
494
  removed_rel.each do |rel|
495
- source = rel[0]
496
- target = rel[1]
495
+ source = rel.node[0]
496
+ target = rel.node[1]
497
497
  h = @pathway.graph[source]
498
498
  h.delete(target) if h
499
499
  h = @pathway.graph[target]
@@ -529,7 +529,7 @@ module Bio
529
529
  _clear_cache
530
530
  @pathway.relations.each do |rel|
531
531
  newedge = yield rel.node[0], rel.node[1], rel.relation
532
- rel.relation = newedge
532
+ rel.edge = newedge
533
533
  @pathway.append(rel, false)
534
534
  end
535
535
  self
data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb CHANGED
@@ -21,6 +21,11 @@ class AlignedStrands
21
21
  extend CutSymbol
22
22
  extend StringFormatting
23
23
 
24
+ # Creates a new object.
25
+ # ---
26
+ # *Returns*:: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands object
27
+ def initialize; super; end
28
+
24
29
  # The object returned for alignments
25
30
  Result = Struct.new(:primary, :complement)
26
31
 
data/lib/bio/version.rb CHANGED
@@ -10,7 +10,7 @@
10
10
  module Bio
11
11
 
12
12
  # BioRuby version (Array containing Integer)
13
- BIORUBY_VERSION = [1, 4, 0].extend(Comparable).freeze
13
+ BIORUBY_VERSION = [1, 4, 1].extend(Comparable).freeze
14
14
 
15
15
  # Extra version specifier (String or nil).
16
16
  # Existance of the value indicates pre-release version or modified version.
data/setup.rb CHANGED
@@ -1472,6 +1472,11 @@ class Installer
1472
1472
  rescue LoadError
1473
1473
  setup_rb_error 'test/unit cannot loaded. You need Ruby 1.8 or later to invoke this task.'
1474
1474
  end
1475
+ ########## begin customization for BioRuby
1476
+ unless defined?(Test::Unit::AutoRunner) then
1477
+ setup_rb_error 'Sorry it does not work in Ruby 1.9. Run "ruby test/runner.rb" instead.'
1478
+ end
1479
+ ########## end customization for BioRuby
1475
1480
  runner = Test::Unit::AutoRunner.new(true)
1476
1481
  runner.to_run << TESTDIR
1477
1482
  runner.run
data/test/data/KEGG/K02338.orthology CHANGED
@@ -1,19 +1,25 @@
1
1
  ENTRY K02338 KO
2
2
  NAME DPO3B, dnaN
3
3
  DEFINITION DNA polymerase III subunit beta [EC:2.7.7.7]
4
+ PATHWAY ko00230 Purine metabolism
5
+ ko00240 Pyrimidine metabolism
6
+ ko03030 DNA replication
7
+ ko03430 Mismatch repair
8
+ ko03440 Homologous recombination
9
+ MODULE M00597 DNA polymerase III complex
4
10
  CLASS Metabolism; Nucleotide Metabolism; Purine metabolism [PATH:ko00230]
5
11
  Metabolism; Nucleotide Metabolism; Pyrimidine metabolism
6
12
  [PATH:ko00240]
7
13
  Genetic Information Processing; Replication and Repair; DNA
8
14
  replication [PATH:ko03030]
15
+ Genetic Information Processing; Replication and Repair; DNA
16
+ replication proteins [BR:ko03032]
9
17
  Genetic Information Processing; Replication and Repair; Mismatch
10
18
  repair [PATH:ko03430]
11
19
  Genetic Information Processing; Replication and Repair; Homologous
12
20
  recombination [PATH:ko03440]
13
- Protein Families; Genetic Information Processing; DNA replication
14
- proteins [BR:ko03032]
15
- Protein Families; Genetic Information Processing; DNA repair and
16
- recombination proteins [BR:ko03400]
21
+ Genetic Information Processing; Replication and Repair; DNA repair
22
+ and recombination proteins [BR:ko03400]
17
23
  DBLINKS RN: R00375 R00376 R00377 R00378
18
24
  COG: COG0592
19
25
  GO: 0003887
@@ -45,9 +51,14 @@ GENES ECO: b3701(dnaN)
45
51
  EBL: B21_03528(dnaN)
46
52
  EBD: ECBD_0002
47
53
  EBR: ECB_03584(dnaN)
54
+ EOH: ECO103_4457(dnaN)
55
+ EOI: ECO111_4528(dnaN)
56
+ EOJ: ECO26_4881(dnaN)
57
+ EOK: G2583_4490(dnaN)
48
58
  EFE: EFER_3996(dnaN)
49
59
  STY: STY3941(dnaN)
50
60
  STT: t3682(dnaN)
61
+ STM: STM3837(dnaN)
51
62
  SPT: SPA3681(dnaN)
52
63
  SEK: SSPA3436
53
64
  SPQ: SPAB_04776
@@ -61,14 +72,14 @@ GENES ECO: b3701(dnaN)
61
72
  SEG: SG3594(dnaN)
62
73
  SET: SEN3654(dnaN)
63
74
  SES: SARI_03808
64
- STM: STM3837(dnaN)
65
75
  YPE: YPO4096(dnaN)
66
76
  YPK: y4112(dnaN)
67
77
  YPM: YP_4004(dnaN)
68
78
  YPA: YPA_4142
69
79
  YPN: YPN_3954
70
- YPP: YPDSF_0002
71
80
  YPG: YpAngola_A4176(dnaN)
81
+ YPP: YPDSF_0002
82
+ YPZ: YPZ3_3515(dnaN)
72
83
  YPS: YPTB3942(dnaN)
73
84
  YPI: YpsIP31758_4152(dnaN)
74
85
  YPY: YPK_0002
@@ -83,7 +94,11 @@ GENES ECO: b3701(dnaN)
83
94
  SDY: SDY_4183(dnaN)
84
95
  ECA: ECA4440(dnaN)
85
96
  PCT: PC1_0002
97
+ PWA: Pecwa_0002
86
98
  ETA: ETA_34520(dnaN)
99
+ EPY: EpC_36690(dnaN)
100
+ EAM: EAMY_3677(dnaN)
101
+ EAY: EAM_3452(dnaN)
87
102
  PLU: plu0002(dnaN)
88
103
  PAY: PAU_00002(dnaN)
89
104
  BUC: BU011(dnaN)
@@ -96,18 +111,25 @@ GENES ECO: b3701(dnaN)
96
111
  SGL: SG0002
97
112
  ENT: Ent638_0002
98
113
  ESA: ESA_03975
114
+ CTU: Ctu_00390(dnaN)
99
115
  KPN: KPN_04104(dnaN)
100
116
  KPE: KPK_0002(dnaN)
101
117
  KPU: KP1_5482(dnaN)
118
+ KVA: Kvar_0006
102
119
  CKO: CKO_00047
120
+ CRO: ROD_40261(dnaN)
103
121
  SPE: Spro_0033
104
122
  PMR: PMI3133(dnaN)
105
123
  EIC: NT01EI_0002
124
+ ETR: ETAE_0002(dnaN)
106
125
  BFL: Bfl016(dnaN)
107
126
  BPN: BPEN_015(dnaN)
108
127
  HDE: HDEF_1740(dnaN)
109
128
  DDA: Dd703_0002
129
+ DDC: Dd586_0002
110
130
  DZE: Dd1591_0002
131
+ XBO: XBJ1_0002(dnaN)
132
+ PAM: PANA_0089(dnaN)
111
133
  HIN: HI0992(dnaN)
112
134
  HIT: NTHI1166(dnaN)
113
135
  HIP: CGSHiEE_07005
@@ -123,6 +145,7 @@ GENES ECO: b3701(dnaN)
123
145
  APA: APP7_0002
124
146
  ASU: Asuc_0002
125
147
  AAP: NT05HA_0052
148
+ AAT: D11S_1973
126
149
  XFA: XF0002
127
150
  XFT: PD0002(dnaN)
128
151
  XFM: Xfasm12_0002
@@ -135,6 +158,7 @@ GENES ECO: b3701(dnaN)
135
158
  XOO: XOO0002(dnaN)
136
159
  XOM: XOO_0002
137
160
  XOP: PXO_03482(dnaN)
161
+ XAL: XALc_0002(dnaN)
138
162
  SML: Smlt0002(dnaN)
139
163
  SMT: Smal_0002
140
164
  VCH: VC0013
@@ -146,6 +170,7 @@ GENES ECO: b3701(dnaN)
146
170
  VPA: VP0012
147
171
  VHA: VIBHAR_00443
148
172
  VSP: VS_0011
173
+ VEX: VEA_002008
149
174
  VFI: VF_0010(dnaN)
150
175
  VFM: VFMJ11_0010(dnaN)
151
176
  VSA: VSAL_I0010(dnaN)
@@ -198,6 +223,7 @@ GENES ECO: b3701(dnaN)
198
223
  SHL: Shal_0002
199
224
  SWD: Swoo_0002
200
225
  SWP: swp_0016
226
+ SVO: SVI_0032(dnaN)
201
227
  ILO: IL0002(dnaN)
202
228
  CPS: CPS_0002(dnaN)
203
229
  PHA: PSHAa0002(dnaN)
@@ -216,8 +242,9 @@ GENES ECO: b3701(dnaN)
216
242
  LPF: lpl0002(dnaN)
217
243
  LPP: lpp0002(dnaN)
218
244
  LPC: LPC_0002(dnaN)
245
+ LLO: LLO_0002(dnaN)
219
246
  MCA: MCA3032(dnaN)
220
- FTU: FTT0002(dnaN)
247
+ FTU: FTT_0002(dnaN)
221
248
  FTF: FTF0002(dnaN)
222
249
  FTW: FTW_0002(dnaN)
223
250
  FTL: FTL_0002
@@ -228,9 +255,13 @@ GENES ECO: b3701(dnaN)
228
255
  FPH: Fphi_0843
229
256
  TCX: Tcr_0002
230
257
  NOC: Noc_0002
258
+ NHL: Nhal_0002
259
+ ALV: Alvin_0002
231
260
  AEH: Mlg_0002
232
261
  HHA: Hhal_1226
233
262
  TGR: Tgr7_0002
263
+ TKM: TK90_0002
264
+ HNA: Hneap_0002
234
265
  HCH: HCH_00003(dnaN)
235
266
  CSA: Csal_0002
236
267
  ABO: ABO_0002(dnaN)
@@ -245,8 +276,8 @@ GENES ECO: b3701(dnaN)
245
276
  RMA: Rmag_0002
246
277
  VOK: COSY_0002(dnaN)
247
278
  KKO: Kkor_0002
248
- NME: NMB1902(dnaN)
249
279
  NMA: NMA0553(dnaN)
280
+ NME: NMB1902(dnaN)
250
281
  NMC: NMC0321(dnaN)
251
282
  NMN: NMCC_0318(dnaN)
252
283
  NMI: NMO_0268(dnaN)
@@ -297,10 +328,11 @@ GENES ECO: b3701(dnaN)
297
328
  PNA: Pnap_4118
298
329
  AAV: Aave_0002
299
330
  AJS: Ajs_4145
331
+ DIA: Dtpsy_0002
300
332
  VEI: Veis_0002
301
333
  DAC: Daci_0002
302
- DIA: Dtpsy_0002
303
334
  VAP: Vapar_0002
335
+ CTT: CtCNB1_0002
304
336
  MPT: Mpe_A0002
305
337
  HAR: HEAR0003(dnaN)
306
338
  MMS: mma_0002(dnaN)
@@ -316,6 +348,8 @@ GENES ECO: b3701(dnaN)
316
348
  MFA: Mfla_0002
317
349
  MMB: Mmol_0002
318
350
  MEI: Msip34_0002
351
+ APP: CAP2UW1_0002
352
+ SLT: Slit_0002
319
353
  HPY: HP0500
320
354
  HPJ: jhp0452(dnaN)
321
355
  HPA: HPAG1_0476
@@ -325,6 +359,7 @@ GENES ECO: b3701(dnaN)
325
359
  HPB: HELPY_0852(dnaN)
326
360
  HHE: HH1126(dnaN)
327
361
  HAC: Hac_0821(dnaN)
362
+ HMS: HMU00020(dnaN)
328
363
  WSU: WS0001(dnaN)
329
364
  TDN: Suden_0002
330
365
  CJE: Cj0002(dnaN)
@@ -338,6 +373,7 @@ GENES ECO: b3701(dnaN)
338
373
  CCO: CCC13826_1851(dnaN)
339
374
  CLA: Cla_0002(dnaN)
340
375
  ABU: Abu_0002(dnaN)
376
+ SDL: Sdel_0004
341
377
  NIS: NIS_0002(dnaN)
342
378
  SUN: SUN_0002(dnaN)
343
379
  NAM: NAMH_0002(dnaN)
@@ -356,8 +392,10 @@ GENES ECO: b3701(dnaN)
356
392
  DDE: Dde_0002
357
393
  DDS: Ddes_0004
358
394
  DMA: DMR_00020(dnaN)
395
+ DSA: Desal_3784
359
396
  LIP: LI0786(dnaN)
360
397
  DBA: Dbac_3096
398
+ DRT: Dret_2471
361
399
  BBA: Bd0002(dnaN)
362
400
  DPS: DP0648
363
401
  DOL: Dole_0094
@@ -369,6 +407,7 @@ GENES ECO: b3701(dnaN)
369
407
  ANK: AnaeK_0002
370
408
  MXA: MXAN_0236(dnaN)
371
409
  SCL: sce8164(dnaN)
410
+ HOH: Hoch_0002
372
411
  SAT: SYN_02050
373
412
  SFU: Sfum_2688
374
413
  RPR: RP419
@@ -381,6 +420,7 @@ GENES ECO: b3701(dnaN)
381
420
  RRJ: RrIowa_0695
382
421
  RMS: RMA_0600(dnaN)
383
422
  RPK: RPR_05615
423
+ RAF: RAF_ORF0544(dnaN)
384
424
  RBE: RBE_0656(dnaN)
385
425
  RBO: A1I_04260
386
426
  OTS: OTBS_0002(dnaN)
@@ -391,6 +431,7 @@ GENES ECO: b3701(dnaN)
391
431
  WPI: WPa_0934(dnaN)
392
432
  AMA: AM1014(dnaN)
393
433
  AMF: AMF_773(dnaN)
434
+ ACN: ACIS_00336(dnaN)
394
435
  APH: APH_1097(dnaN)
395
436
  ERU: Erum7880(dnaN)
396
437
  ERW: ERWE_CDS_08330(dnaN)
@@ -415,7 +456,7 @@ GENES ECO: b3701(dnaN)
415
456
  RLT: Rleg2_4329
416
457
  RLG: Rleg_4592
417
458
  RHI: NGR_c36750(dnaN)
418
- LAS: CLIBASIA_01695
459
+ LAS: CLIBASIA_01695(dnaA)
419
460
  BME: BMEI1942
420
461
  BMF: BAB1_0002(dnaN)
421
462
  BMB: BruAb1_0002(dnaN)
@@ -465,33 +506,36 @@ GENES ECO: b3701(dnaN)
465
506
  RSH: Rsph17029_0012
466
507
  RSQ: Rsph17025_0003
467
508
  RSK: RSKD131_2743
509
+ RCP: RCAP_rcc00002(dnaN)
468
510
  JAN: Jann_0002
469
511
  RDE: RD1_0209(dnaN)
470
512
  PDE: Pden_0342 Pden_0970 Pden_2834
471
- DSH: Dshi_3374
513
+ DSH: Dshi_3374(dnaN)
472
514
  MMR: Mmar10_0002
473
515
  HNE: HNE_0563(dnaN)
474
516
  HBA: Hbal_3037
475
- ZMO: ZMO0980(dnaN)
517
+ ZMO: ZMO0980
518
+ ZMN: Za10_0322
476
519
  NAR: Saro_0639 Saro_1429
477
520
  SAL: Sala_0708
478
521
  SWI: Swit_2795
522
+ SJP: SJA_C1-09100(dnaN)
479
523
  ELI: ELI_07330
480
524
  GOX: GOX0002
481
525
  GBE: GbCGDNIH1_0319
482
526
  ACR: Acry_1437
483
- GDI: GDI1772(dnaN)
527
+ GDI: GDI_1772(dnaN)
484
528
  GDJ: Gdia_0002
529
+ APT: APA01_12310
485
530
  RRU: Rru_A0002
486
531
  RCE: RC1_3063(dnaN)
487
532
  MAG: amb0637
533
+ AZL: AZL_027260(dnaN)
534
+ APB: SAR116_1557
488
535
  MGM: Mmc1_0002
489
- ABA: Acid345_0002
490
- ACA: ACP_2196(dnaN)
491
- SUS: Acid_0002
492
536
  BSU: BSU00020(dnaN)
493
537
  BHA: BH0002(dnaN)
494
- BAN: BA0002(dnaN-1) BA2684(dnaN-2)
538
+ BAN: BA_0002(dnaN-1) BA_2684(dnaN-2)
495
539
  BAR: GBAA0002(dnaN-1) GBAA2684(dnaN-2)
496
540
  BAA: BA_0597 BA_3202
497
541
  BAT: BAS0002 BAS2499
@@ -515,42 +559,54 @@ GENES ECO: b3701(dnaN)
515
559
  BCL: ABC0002(dnaN)
516
560
  BAY: RBAM_000020(dnaN)
517
561
  BPU: BPUM_0002(dnaN)
562
+ BPF: BpOF4_07960
563
+ BMQ: BMQ_0002(dnaN)
518
564
  OIH: OB0002(dnaN)
519
565
  GKA: GK0002(dnaN)
520
566
  GTN: GTNG_0002
521
567
  GWC: GWCH70_0002
568
+ GYM: GYMC10_0002
569
+ GYC: GYMC61_0002
522
570
  AFL: Aflv_0002(dnaN)
523
571
  SAU: SA0002(dnaN)
524
572
  SAV: SAV0002(dnaN)
525
573
  SAW: SAHV_0002(dnaN)
574
+ SAH: SaurJH1_0002
575
+ SAJ: SaurJH9_0002
526
576
  SAM: MW0002(dnaN)
527
- SAR: SAR0002(dnaN)
528
577
  SAS: SAS0002
578
+ SAR: SAR0002(dnaN)
529
579
  SAC: SACOL0002(dnaN)
530
- SAB: SAB0002(dnaN)
531
- SAA: SAUSA300_0002(dnaN)
532
580
  SAX: USA300HOU_0002(dnaN)
581
+ SAA: SAUSA300_0002(dnaN)
533
582
  SAO: SAOUHSC_00002
534
- SAJ: SaurJH9_0002
535
- SAH: SaurJH1_0002
536
583
  SAE: NWMN_0002(dnaN)
584
+ SAD: SAAV_0002(dnaN)
585
+ SAB: SAB0002(dnaN)
537
586
  SEP: SE0002
538
587
  SER: SERP2552(dnaN)
539
588
  SHA: SH0002(dnaN)
540
589
  SSP: SSP0002
541
590
  SCA: Sca_2473(dnaN)
591
+ SLG: SLGD_02547
542
592
  LMO: lmo0002(dnaN)
543
593
  LMF: LMOf2365_0002(dnaN)
544
594
  LMH: LMHCC_2662(dnaN)
545
595
  LMC: Lm4b_00002(dnaN)
596
+ LMN: LM5578_3021(dnaN)
597
+ LMY: LM5923_2970(dnaN)
546
598
  LIN: lin0002(dnaN)
547
599
  LWE: lwe0002(dnaN)
600
+ LSG: lse_0002(dnaN)
548
601
  LSP: Bsph_0005(dnaN) Bsph_p018
549
602
  ESI: Exig_0002
550
603
  EAT: EAT1b_1729
551
604
  MCL: MCCL_0002(dnaN)
552
605
  BBE: BBR47_00020(dnaN)
606
+ PJD: Pjdr2_0002
607
+ AAC: Aaci_0002 Aaci_0484
553
608
  LLA: L0275(dnaN)
609
+ LLK: LLKF_0002(dnaN)
554
610
  LLC: LACR_0002
555
611
  LLM: llmg_0002(dnaN)
556
612
  SPY: SPy_0003(dnaN)
@@ -581,6 +637,7 @@ GENES ECO: b3701(dnaN)
581
637
  SAN: gbs0002(dnaN)
582
638
  SAK: SAK_0002(dnaN)
583
639
  SMU: SMU.02(dnaN)
640
+ SMC: SmuNN2025_0002(dnaN)
584
641
  STC: str0002(dnaN)
585
642
  STL: stu0002(dnaN)
586
643
  STE: STER_0002
@@ -596,9 +653,12 @@ GENES ECO: b3701(dnaN)
596
653
  SEU: SEQ_0002
597
654
  SUB: SUB0002(dnaN)
598
655
  SDS: SDEG_0002(dnaN)
656
+ SGA: GALLO_0002(dnaN)
657
+ SMB: smi_0002(dnaN)
599
658
  LPL: lp_0002(dnaN)
600
659
  LPJ: JDM1_0002(dnaN)
601
660
  LJO: LJ0002
661
+ LJF: FI9785_64(dnaN)
602
662
  LAC: LBA0002(dnaN)
603
663
  LSA: LSA0002(dnaN)
604
664
  LSL: LSL_0002(dnaN)
@@ -612,6 +672,8 @@ GENES ECO: b3701(dnaN)
612
672
  LRF: LAR_0002
613
673
  LHE: lhv_0002
614
674
  LFE: LAF_0002
675
+ LRH: LGG_00002(dnaN)
676
+ LRL: LC705_00002(dnaN)
615
677
  PPE: PEPE_0002
616
678
  EFA: EF0002(dnaN)
617
679
  OOE: OEOE_0002
@@ -625,6 +687,7 @@ GENES ECO: b3701(dnaN)
625
687
  CNO: NT01CX_0866(dnaN)
626
688
  CTH: Cthe_2372
627
689
  CDF: CD0002(dnaN)
690
+ CDC: CD196_0002(dnaN)
628
691
  CBO: CBO0002(dnaG)
629
692
  CBA: CLB_0002(dnaN)
630
693
  CBH: CLC_0002(dnaN)
@@ -632,7 +695,7 @@ GENES ECO: b3701(dnaN)
632
695
  CBL: CLK_3134(dnaN) CLK_A0115(dnaN)
633
696
  CBK: CLL_A0002(dnaN)
634
697
  CBB: CLD_0824(dnaN) CLD_A0160(dnaN)
635
- CBI: CLJ_B0002(dnaN_1)
698
+ CBI: CLJ_0039(dnaN_2) CLJ_B0002(dnaN_1)
636
699
  CBT: CLH_0002(dnaN)
637
700
  CBF: CLI_0002(dnaN)
638
701
  CBE: Cbei_0002
@@ -644,21 +707,28 @@ GENES ECO: b3701(dnaN)
644
707
  AOE: Clos_0002
645
708
  STH: STH2
646
709
  SWO: Swol_0002
710
+ VPR: Vpar_0002
711
+ AFN: Acfer_0004
647
712
  ATE: Athe_0003
648
713
  DSY: DSY0002(dnaN)
649
714
  DHD: Dhaf_0002
650
715
  DRM: Dred_0002
716
+ DAE: Dtox_0002
651
717
  PTH: PTH_0002(dnaN)
652
718
  DAU: Daud_0002
653
719
  HMO: HM1_0904(dnaN)
654
720
  FMA: FMG_0002
721
+ APR: Apre_0002
655
722
  EEL: EUBELI_00002
656
723
  ERE: EUBREC_0002
724
+ CLO: HMPREF0868_0092(dnaN)
657
725
  TTE: TTE0002(dnaN)
658
726
  TEX: Teth514_0002
659
727
  TPD: Teth39_0002
728
+ TIT: Thit_0002
660
729
  CHY: CHY_2709(dnaN)
661
730
  MTA: Moth_0003
731
+ ADG: Adeg_0002 Adeg_0689
662
732
  CSC: Csac_0002
663
733
  CPO: COPRO5265_0066(dnaN)
664
734
  NTH: Nther_0002
@@ -676,12 +746,15 @@ GENES ECO: b3701(dnaN)
676
746
  MSY: MS53_0002(dnaN)
677
747
  MCP: MCAP_0002(dnaN)
678
748
  MAA: MAG_0020(dnaN)
749
+ MAL: MAGa0020(dnaN)
679
750
  MAT: MARTH_orf003(dnaN)
680
751
  MCO: MCJ_000020(dnaN)
752
+ MHO: MHO_0050(dnaN)
753
+ MCD: MCRO_0002(dnaN)
681
754
  UUR: UU079(dnaN)
682
755
  UPA: UPA3_0078(dnaN)
683
756
  UUE: UUR10_0085(dnaN)
684
- POY: PAM002(dnaN)
757
+ POY: PAM_002(dnaN)
685
758
  AYW: AYWB_002(dnaN)
686
759
  PML: ATP_00194(dnaN)
687
760
  PAL: PAa_0002(dnaN)
@@ -720,9 +793,11 @@ GENES ECO: b3701(dnaN)
720
793
  RHA: RHA1_ro03667(dnaN)
721
794
  RER: RER_00020(dnaN)
722
795
  ROP: ROP_34840(dnaN)
796
+ GBR: Gbro_0002
723
797
  SCO: SCO3878(dnaN) SCP1.119(dnaN)
724
798
  SMA: SAV_3362(dnaN2) SAV_4317(dnaN1)
725
799
  SGR: SGR_3397(dnaN2) SGR_3701(dnaN)
800
+ SCB: SCAB_45811(dnaN)
726
801
  TWH: TWT002(dnaN)
727
802
  TWS: TW002(dnaN)
728
803
  LXX: Lxx00020(dnaN)
@@ -734,22 +809,32 @@ GENES ECO: b3701(dnaN)
734
809
  RSA: RSal33209_0002
735
810
  KRH: KRH_00020(dnaN)
736
811
  MLU: Mlut_00020
812
+ RMU: RMDY18_00020
737
813
  BCV: Bcav_0002
738
814
  BFA: Bfae_00020
739
815
  JDE: Jden_0002
740
816
  KSE: Ksed_00020
817
+ XCE: Xcel_0002
741
818
  PAC: PPA0002
742
819
  NCA: Noca_0002
820
+ KFL: Kfla_0002
743
821
  TFU: Tfu_0002 Tfu_0086
822
+ TCU: Tcur_0002
823
+ SRO: Sros_0002
744
824
  FRA: Francci3_0003 Francci3_0738 Francci3_1710
745
825
  FRE: Franean1_0003 Franean1_2567 Franean1_5871
746
826
  FAL: FRAAL0004(dnaN) FRAAL1257
747
827
  ACE: Acel_0002
828
+ NML: Namu_0002
829
+ GOB: Gobs_0002
748
830
  KRA: Krad_0002 Krad_1769
749
831
  SEN: SACE_0003(dnaN) SACE_0327(dnaN)
832
+ SVI: Svir_00020
750
833
  AMI: Amir_0002 Amir_0251
751
834
  STP: Strop_0003
752
835
  SAQ: Sare_0002
836
+ CAI: Caci_0002
837
+ SNA: Snas_0002
753
838
  BLO: BL0638(dnaN)
754
839
  BLJ: BLD_1435(dnaN)
755
840
  BLN: Blon_0003
@@ -757,16 +842,15 @@ GENES ECO: b3701(dnaN)
757
842
  BLA: BLA_0002(dnaN)
758
843
  BLC: Balac_0002
759
844
  BLT: Balat_0002
845
+ BDE: BDP_0002
846
+ GVA: HMPREF0424_0044(dnaN)
760
847
  RXY: Rxyl_0002
848
+ CWO: Cwoe_0002
761
849
  AFO: Afer_0002
762
850
  CCU: Ccur_00020
763
- FNU: FN0536 FN0617
764
- LBA: Lebu_1267
765
- GAU: GAU_0002(dnaN)
766
- RBA: RB10108(dnaN)
767
- OTE: Oter_0953
768
- MIN: Minf_0002(dnaN)
769
- AMU: Amuc_0816
851
+ SHI: Shel_00020
852
+ APV: Apar_0003
853
+ ELE: Elen_0003
770
854
  CTR: CT075(dnaN)
771
855
  CTA: CTA_0080(dnaN)
772
856
  CTB: CTL0331(dnaN)
@@ -799,6 +883,54 @@ GENES ECO: b3701(dnaN)
799
883
  LBI: LEPBI_I0002(dnaN)
800
884
  LBF: LBF_0005(dnaN)
801
885
  BHY: BHWA1_01258(dnaN)
886
+ ABA: Acid345_0002
887
+ ACA: ACP_2196(dnaN)
888
+ SUS: Acid_0002
889
+ BTH: BT_1364
890
+ BFR: BF2981
891
+ BFS: BF2857
892
+ BVU: BVU_2894
893
+ PGI: PG1853(dnaN)
894
+ PGN: PGN_1786
895
+ PDI: BDI_0694
896
+ APS: CFPG_644
897
+ PRU: PRU_0839(dnaN)
898
+ SRU: SRU_0002(dnaN)
899
+ SRM: SRM_00003(dnaN)
900
+ RMR: Rmar_0002
901
+ CHU: CHU_1549(dnaN)
902
+ DFE: Dfer_3720
903
+ SLI: Slin_4880
904
+ CPI: Cpin_0616
905
+ PHE: Phep_3235
906
+ GFO: GFO_1914(dnaN)
907
+ FJO: Fjoh_2720
908
+ FPS: FP1091(dnaN)
909
+ FBA: FIC_00920
910
+ COC: Coch_1752
911
+ RBI: RB2501_13564
912
+ SMG: SMGWSS_005(dnaN)
913
+ SMS: SMDSEM_005(dnaN)
914
+ SMH: DMIN_00040
915
+ BBL: BLBBGE_048(dnaN)
916
+ BPI: BPLAN_585(dnaN)
917
+ AAS: Aasi_0152
918
+ FSU: Fisuc_1334
919
+ FNU: FN0536 FN0617
920
+ LBA: Lebu_1267
921
+ STR: Sterm_2002
922
+ SMF: Smon_0578
923
+ OTE: Oter_0953
924
+ CAA: Caka_2082
925
+ MIN: Minf_0002(dnaN)
926
+ AMU: Amuc_0816
927
+ GAU: GAU_0002(dnaN)
928
+ RBA: RB10108(dnaN)
929
+ PSL: Psta_1042
930
+ EMI: Emin_0003
931
+ RSD: TGRD_004
932
+ TAI: Taci_0002
933
+ ACO: Amico_0002
802
934
  SYN: slr0965(dnaN)
803
935
  SYW: SYNW0001(dnaN)
804
936
  SYC: syc1496_c(dnaN)
@@ -817,6 +949,8 @@ GENES ECO: b3701(dnaN)
817
949
  CYP: PCC8801_1016
818
950
  CYC: PCC7424_0340
819
951
  CYN: Cyan7425_0199
952
+ CYH: Cyan8802_1045
953
+ CYU: UCYN_01290
820
954
  GVI: gvip446(dnaN)
821
955
  ANA: alr2010(dnaN) alr7569
822
956
  NPU: Npun_R0034
@@ -835,25 +969,6 @@ GENES ECO: b3701(dnaN)
835
969
  PME: NATL1_00001(dnaN)
836
970
  TER: Tery_0008
837
971
  AMR: AM1_3096(dnaN)
838
- BTH: BT_1364
839
- BFR: BF2981
840
- BFS: BF2857
841
- BVU: BVU_2894
842
- PGI: PG1853(dnaN)
843
- PGN: PGN_1786
844
- PDI: BDI_0694
845
- APS: CFPG_644
846
- SRU: SRU_0002(dnaN)
847
- CHU: CHU_1549(dnaN)
848
- CPI: Cpin_0616
849
- GFO: GFO_1914(dnaN)
850
- FJO: Fjoh_2720
851
- FPS: FP1091(dnaN)
852
- FBA: FIC_00920
853
- COC: Coch_1752
854
- SMG: SMGWSS_005(dnaN)
855
- SMS: SMDSEM_005(dnaN)
856
- AAS: Aasi_0152
857
972
  CTE: CT0001(dnaN)
858
973
  CPC: Cpar_0002
859
974
  CCH: Cag_0002
@@ -868,6 +983,8 @@ GENES ECO: b3701(dnaN)
868
983
  DET: DET1227(dnaN)
869
984
  DEH: cbdb_A1145(dnaN)
870
985
  DEB: DehaBAV1_1036
986
+ DEV: DhcVS_1009(dnaN)
987
+ DEG: DehalGT_0967
871
988
  RRS: RoseRS_4406
872
989
  RCA: Rcas_0749
873
990
  CAU: Caur_2639
@@ -875,15 +992,17 @@ GENES ECO: b3701(dnaN)
875
992
  CHL: Chy400_2852
876
993
  HAU: Haur_1513
877
994
  TRO: trd_0714(dnaN)
878
- EMI: Emin_0003
879
- RSD: TGRD_004
995
+ STI: Sthe_1312
880
996
  DRA: DR_0001
881
997
  DGE: Dgeo_0003 Dgeo_3063
882
998
  DDR: Deide_00020(dnaN)
883
999
  TTH: TTC1609
884
1000
  TTJ: TTHA0001
1001
+ MRB: Mrub_0002
885
1002
  AAE: aq_1882(dnaN)
886
1003
  HYA: HY04AAS1_1088
1004
+ HTH: HTH_0569(dnaN)
1005
+ TAL: Thal_1223
887
1006
  SUL: SYO3AOP1_0963
888
1007
  SAF: SULAZ_0725(dnaN)
889
1008
  PMX: PERMA_1539(dnaN)
@@ -892,6 +1011,7 @@ GENES ECO: b3701(dnaN)
892
1011
  TLE: Tlet_0486
893
1012
  TRQ: TRQ2_0686
894
1013
  TNA: CTN_0424
1014
+ TNP: Tnap_0892
895
1015
  TME: Tmel_0535
896
1016
  TAF: THA_1368(dnaN)
897
1017
  FNO: Fnod_1203
@@ -900,3 +1020,11 @@ GENES ECO: b3701(dnaN)
900
1020
  DTH: DICTH_1442(dnaN)
901
1021
  DTU: Dtur_1551
902
1022
  TYE: THEYE_A0016(dnaN)
1023
+ TTR: Tter_0993
1024
+ DDF: DEFDS_0001(dnaN)
1025
+ DAP: Dacet_2869
1026
+ REFERENCE PMID:8087839
1027
+ AUTHORS Stillman B.
1028
+ TITLE Smart machines at the DNA replication fork.
1029
+ JOURNAL Cell 78:725-8 (1994)
1030
+ ///