bio 1.4.0 → 1.4.1

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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
+ ///