PHD sequence format

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Description

The phd format is created by PHRED to store serialized chromatogram data.

This file format can be parsed by the Bio::SeqIO system using the Bio::SeqIO::phd module.

Example

BEGIN_SEQUENCE ML4924R

BEGIN_COMMENT

CHROMAT_FILE: ML4924R
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8792
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
a 6 1
c 6 20
t 6 17
t 8 26
t 8 35
g 12 48
g 18 58
t 16 66
c 14 83
g 11 98
c 9 104
c 6 122
t 6 128
g 9 140
c 19 147
a 20 159
g 32 167
g 34 178
t 34 190
a 39 200
c 39 208
c 39 221
g 29 233
g 40 243
t 28 255
c 21 267
c 13 277
g 4 288
n 4 297
g 4 298
a 8 314
t 8 328
t 23 339
c 29 349
c 39 359
c 40 369
g 40 381
g 40 390
g 40 401
t 46 413
c 34 425
g 33 436
a 29 447
c 29 453
c 32 466
c 33 476
a 34 485
c 34 492
g 34 505
c 34 514
g 40 527
t 40 537
c 34 548
c 34 559
g 34 572
c 34 579
t 34 592
t 34 602
t 39 613
g 40 625
c 40 633
t 40 645
c 40 656
a 40 664
t 40 673
c 40 685
t 46 697
c 51 707
c 51 718
c 56 728
t 51 738
c 51 749
t 35 760
g 35 772
a 35 783
c 35 790
t 35 803
t 35 813
t 39 824
g 40 836
c 40 844
a 40 855
t 40 865
c 56 876
c 42 887
c 51 898
t 46 909
t 46 921
a 46 931
a 46 940
t 46 951
c 46 962
c 46 974
t 46 985
c 40 995
a 40 1004
g 40 1015
a 40 1028
a 40 1037
t 40 1048
g 35 1060
g 35 1071
c 35 1080
g 35 1096
t 35 1106
c 35 1116
a 40 1125
g 40 1138
a 40 1150
g 51 1160
a 51 1172
a 51 1182
g 51 1193
a 40 1204
a 35 1214
g 35 1226
c 39 1235
t 39 1250
c 39 1259
t 39 1272
c 40 1282
g 51 1295
a 51 1305
a 51 1315
c 51 1325
c 51 1337
c 51 1348
a 51 1358
a 51 1368
t 51 1381
g 51 1393
a 51 1403
g 51 1415
g 51 1427
g 39 1440
a 39 1450
t 39 1462
a 39 1470
t 39 1483
c 35 1494
a 40 1503
a 40 1514
g 40 1528
g 40 1540
t 40 1552
t 39 1565
c 39 1574
a 39 1583
g 39 1598
a 38 1609
a 40 1619
g 39 1632
c 39 1642
t 39 1657
c 39 1666
g 39 1680
t 40 1691
t 45 1703
c 51 1713
t 51 1726
c 51 1736
a 51 1746
a 51 1757
c 51 1767
a 45 1778
t 45 1791
c 45 1802
t 45 1816
c 45 1826
c 45 1838
g 45 1852
t 51 1863
t 51 1875
g 56 1887
g 43 1899
t 43 1911
g 43 1924
a 43 1933
g 43 1946
a 43 1958
END_DNA

END_SEQUENCE
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