From owner-announce@net.bio.net Fri May 07 23:14:00 1999 Path: biosci!biosci!not-for-mail From: "Victor Solovyev" Newsgroups: bionet.announce Subject: Read and View (Java) ABI trace file, analyze Error positions and polymorphism Date: 7 May 1999 17:14:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 217 Sender: daemon@net.bio.net Approved: kristoff@net.bio.net Distribution: world Message-ID: <9905071736.ZM2602@octane> NNTP-Posting-Host: net.bio.net 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V.V., Salamov A.A. Assignment of base quality and partition of Overcall, Undercall, Miscall and sequence polymorphism (unpublished data). Seledtsov I.A., Solovyev V.V. Visual and computational analysys of ABI trace data (unpublished data).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@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 .