PHD sequence format
From BioPerl
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
