Read and View (Java) ABI trace file,
Victor Solovyev
solovyev at sanger.ac.uk
Wed May 19 12:55:24 EST 1999
We installed ABIQ - Read and View ABI trace file and potential
Error positions
ABIQ Program is prepared to analyze ABi trace files and calculate
error probability for each base using a new version of the approach
described in (Lawrence,Solovyev,1994).
We plan to develop these tools further to use in sequence
EDITING/ASSEMBLING and study of HUMAN POLYMORPHISM.
If we observe different bases in several reads of some locus and
these bases have very small probability of errors, than we have a
good candidate of polymorphic site.
The program compute the PROBABILITY OF 3 TYPES OF BASE CALLING ERRORS
(Insertion - Overcall; deletion - Undercall and substitution - Miscall).
The program can be run at http://genomic.sanger.ac.uk/ of our
Computational Genomic Group WEB server
(http://genomic.sanger.ac.uk/abi/abi.shtml)
This version of program uses ABI base calling sequence, but we
plan to incorparate our version of base calling in the future, also we plan
to tune the quality prediction part for new ABI sequencers.
The Java viewer can be used for visual analysis of Trace files and
quality data.
References:
Solovyev V.V., Salamov A.A. Assignment of base quality and partition of
Overcall,
Undercall, Miscall and sequence polymorphism (unpublished data).
Seledtsov I.A., Solovyev V.V. Visual and computational analysys of ABI trace
data (unpublished data).
Lawrence C.B., Solovyev V.V. Assignment of Position-Specific Error
Probability to primary DNA Sequence Data.Nucl.Acids Res., 1994, 22,
7,1272-1280.
The program output includes :
The sequence and probabilitoes of errors in 0-9 scale corresponding (0 -
100%).
Sequence of ABI base calling in FASTA format
and Quality data for each base: Total quality and Overcall, Undercall and
Miscall, respectively. Quality scale is ( q = -10 Log (p)) similar with
the used in (Ewing and Green,1998, Genome Res.,8,186-194.
Browse --> Load File ---> Show data
Example of output of the program:
A01U0005 " View ABI traces and Quality data " (Java viewer button)
10 20 30 40 50
ACTATCATTAAAGATTCTGTCAATATTTAAAATAAGATGACAGATATAAT
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
60 70 80 90 100
TCATATTGTAGGCTCACATGTAAGCATTAAATAACCGATATACTAAACTA
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
110 120 130 140 150
TGCGATGCCTTCTTTAATCCTTCTTATTTTATTGTAGTCACTAAAATTTT
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
160 170 180 190 200
AGATTGGAATACTGCAGGAACTTAGTACAAGTCAAATGTGTTAATACTAC
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000100000000000000000000
210 220 230 240 250
ACATGGAAAGAATATTAGGAAACAAGCATTTGGTCACCTTCCAGTCATAA
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
260 270 280 290 300
AAGAGACTGAGGCAGAAATAATATGAACCAGGGCTGTATGTTTACCTAAG
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
310 320 330 340 350
ACAGTTGCACATAAGAATCAACTGGGGCATTTAAAACACAGCAACAACAA
P over 00000000000000000000000000000000000000000000000000
P under 00000000000000000000000000000000000000000000000000
P mis 00000000000000000000000000000000000000000000000000
360 370 380 390 400
TAACCCAAACAGTGATCCTGGGGCTCCATTCCAGACCCAACTTAATCAGT
P over 00000300000000000000000000000000000001000000000000
P under 00020000000000000010000000000000000000000000000000
P mis 00100400000000000000000000000000000002000000000000
410 420 430 440 450
ATTTCTGGAGGTTGGACACTGACGGCTGTTATTTTTCAAAGGCATCCCAG
P over 00000000000000000000000010000000000000000100000100
P under 00002100011200000000011000000001000011000000020000
P mis 00000001010000000000010000000000040000000100010200
GGTGGA
P over 000000
P under 000000
P mis 010000
> A01U0005 Length: 456
ACTATCATTAAAGATTCTGTCAATATTTAAAATAAGATGACAGATATAATTCATATTGTA
GGCTCACATGTAAGCATTAAATAACCGATATACTAAACTATGCGATGCCTTCTTTAATCC
TTCTTATTTTATTGTAGTCACTAAAATTTTAGATTGGAATACTGCAGGAACTTAGTACAA
GTCAAATGTGTTAATACTACACATGGAAAGAATATTAGGAAACAAGCATTTGGTCACCTT
CCAGTCATAAAAGAGACTGAGGCAGAAATAATATGAACCAGGGCTGTATGTTTACCTAAG
ACAGTTGCACATAAGAATCAACTGGGGCATTTAAAACACAGCAACAACAATAACCCAAAC
AGTGATCCTGGGGCTCCATTCCAGACCCAACTTAATCAGTATTTCTGGAGGTTGGACACT
GACGGCTGTTATTTTTCAAAGGCATCCCAGGGTGGA
> Total quality A01U0005
99 99 69 49 43 49 69 32 99 69 62 43 99 49 49 99 69 49 69 99
62 49 35 99 69 99 99 99 69 99 40 43 99 62 62 99 49 49 99 99
99 62 49 99 99 99 99 69 49 99 99 99 99 99 69 99 99 99 99 99
69 46 99 99 99 99 99 49 69 99 99 49 99 69 99 62 69 62 69 69
99 99 99 69 69 49 69 99 99 99 99 99 99 99 69 69 99 99 99 69
62 99 99 69 99 62 62 69 40 49 62 99 69 49 99 99 62 62 99 99
49 99 99 69 49 99 99 69 69 99 99 99 99 99 99 99 69 99 99 99
99 49 69 99 69 49 69 99 99 49 99 62 99 40 49 40 40 49 99 99
99 69 69 49 69 62 40 69 49 62 49 35 69 99 49 49 99 69 49 25
49 69 99 99 40 49 69 99 99 69 99 99 69 49 69 99 49 40 99 99
99 62 69 35 49 40 49 49 40 40 40 49 69 99 69 69 69 48 49 40
49 99 62 40 32 49 69 69 49 49 49 35 35 40 69 99 99 69 32 62
69 35 40 62 99 62 99 49 69 99 49 35 40 69 62 99 49 62 40 69
48 99 49 99 69 69 40 62 99 69 99 99 69 69 62 99 99 51 99 62
69 69 40 62 62 62 69 99 99 69 99 69 69 99 69 62 46 49 99 62
62 62 62 62 62 62 62 69 62 62 51 69 62 69 69 99 69 99 62 62
69 69 62 48 48 40 62 69 62 51 99 69 69 99 69 69 62 51 62 51
51 62 46 62 48 40 49 48 40 51 62 51 22 18 40 5 69 69 99 62
40 51 46 40 69 46 31 51 27 48 31 51 49 62 40 28 51 32 62 51
32 39 32 62 39 30 34 13 46 29 31 32 39 62 62 40 62 51 40 40
69 62 33 28 17 26 32 25 28 20 24 15 35 46 40 31 51 32 51 62
39 20 25 30 21 51 51 31 30 46 32 27 35 8 36 26 22 26 29 29
36 19 40 51 46 16 30 14 32 28 39 22 29 30 39 39
> Overcall quality A01U0005
99 99 69 49 43 49 69 32 99 99 69 43 99 49 49 99 99 49 69 99
99 99 35 99 99 99 99 99 99 99 69 43 99 99 69 99 49 49 99 99
99 99 49 99 99 99 99 99 49 99 99 99 99 99 99 99 99 99 99 99
99 49 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 69 99 99
99 99 99 99 99 49 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 69 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 69 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 37
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 37 99 99 10 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 49 99 19 99 32 99 99 99 99 99 99 99 99 99 99
99 99 99 40 99 99 99 43 99 99 99 99 37 99 99 99 99 99 99 99
99 43 99 99 24 99 99 99 99 99 99 99 99 49 99 43 99 99 37 35
99 24 99 99 99 99 99 21 43 37 99 43 99 40 43 43
> Undercall quality A01U0005
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
69 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 69 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
69 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 52 99 99
99 99 69 99 99 99 99 99 99 99 99 99 99 99 99 99 52 99 99 69
99 99 69 69 99 69 69 99 69 99 52 99 69 99 99 99 99 99 69 69
99 99 69 69 69 40 69 99 99 52 99 69 99 99 99 99 99 52 69 52
52 69 52 99 69 40 99 69 40 52 99 52 99 18 69 99 99 99 99 99
40 52 52 40 69 52 40 52 27 69 32 52 99 69 40 32 52 32 69 52
52 40 32 69 40 99 52 99 52 99 32 32 40 69 99 40 69 52 40 40
99 69 99 69 18 27 52 40 32 27 27 16 99 52 40 32 52 32 52 69
52 27 27 32 99 52 52 32 32 52 32 27 69 32 40 32 22 27 99 69
40 99 40 52 52 18 69 52 52 69 52 40 32 52 52 52
> Miscall quality A01U0005
99 99 99 99 99 99 99 99 99 99 69 99 99 99 99 99 99 99 99 99
69 49 99 99 99 99 99 99 99 99 40 99 99 69 69 99 99 99 99 99
99 69 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 49 99 99 99 99 99 49 69 99 99 49 99 99 99 69 69 69 99 69
99 99 99 99 99 69 99 99 99 99 99 99 99 99 69 69 99 99 99 69
69 99 99 99 99 69 69 69 40 49 69 99 69 49 99 99 69 69 99 99
49 99 99 99 49 99 99 69 69 99 99 99 99 99 99 99 99 99 99 99
99 49 69 99 69 49 69 99 99 49 99 69 99 40 49 40 40 49 99 99
99 69 99 49 69 69 40 69 49 69 49 35 69 99 49 49 99 69 49 27
49 69 99 99 40 49 69 99 99 69 99 99 69 49 69 99 49 40 99 99
99 69 69 35 49 40 49 49 40 40 40 49 69 99 69 69 69 49 49 40
49 99 69 40 32 49 69 69 49 49 49 35 35 40 99 99 99 99 32 69
69 35 40 69 99 69 99 49 69 99 49 35 40 69 69 99 49 69 40 69
49 99 49 99 99 69 40 69 99 99 99 99 99 99 69 99 99 69 99 69
69 69 40 69 69 69 99 99 99 99 99 99 99 99 69 69 49 49 99 69
69 69 69 99 69 99 69 99 69 69 99 99 99 69 99 99 99 99 99 69
99 99 69 49 49 99 69 99 69 99 99 99 99 99 99 69 69 99 99 69
99 69 49 69 49 69 49 49 69 99 69 69 23 49 40 9 99 69 99 69
69 99 49 99 99 49 33 99 99 49 49 99 49 99 69 33 69 99 69 99
32 49 99 99 49 30 35 17 49 33 69 69 49 99 69 69 99 99 69 99
99 99 33 30 33 49 33 27 32 23 33 30 49 49 69 49 99 99 69 99
40 23 40 40 30 69 99 69 40 49 99 99 35 9 40 30 49 69 32 32
40 23 69 69 49 27 30 17 35 30 40 23 35 33 49 49
--
Victor Solovyev
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
Email: solovyev at sanger.ac.uk http://genomic.sanger.ac.uk
Phone: 44-1223-494799 FAX: 44-1223-494919
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