54 lines
2.1 KiB
Plaintext
54 lines
2.1 KiB
Plaintext
Extracting Sequences from Trace Files
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Simon Dear
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(sd@mrc-lmb.cam.ac.uk)
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19 November 1992
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To obtain the sequence from a trace file, the program 'trace2seq' can
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be used. It can operate on several trace file sources: ABI 373A
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sample files, Pharmacia A.L.F. traces (created by 'alfsplit') and SCF
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traces (created by 'makeSCF' or from other sources). The sequence is
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stored in a file. A header, required for assembly into the sequence
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assembly programs xdap and xbap, may optionally be produced.
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Usage is as follows:
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trace2seq (-ABI | -ALF | -SCF) {tracefilename}
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-output {outputfilename}
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[-header (0|1)] [-raw filename]
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By default, a header is not produced. To be included, the -header
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option with argument 1, or the -raw option should be used. The -raw
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option allows the trace file name, that forms part of the header, to
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be explicitly specified. By default the trace file name in the header
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is that from from which the sequence came.
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An example:
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To output the sequence from the ABI 373A trace 'trace.abi', with the
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inclusion of a header, into a file called 'abi.seq':
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trace2seq -ABI trace.abi -output abi.seq -header 1
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After the operation, 'abi.seq' will contain:
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; 827 0 827ABI trace.abi
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AG--TGCATGCCTGCAGGTCGACTCTAGAGG-TCCCGGGGTACCGAGCTC
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GAATTC-TAATCATGGTCATAGCTGT-TCCTGTGTGAAATT-TTATCCGC
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TCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGG
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GGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCC
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CGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCC
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AACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCCAGGGTGGTTTTA-T
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TTTCACCAGTGAGACGGGCAACAGCTGATTGCCCTTCACCGCCTGGCCCT
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GAGAGGAGTTGCAGCAAGCGGTCCACGCT-GTT-TGCCCCAGCAGGCG-A
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AATCCTGTTTTGATGGTTGGTTCC-GAAATCGGCAAAAATCCCTTATAAA
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TTC-AAAGGATAGG-CCGAG--TGGGG-T-AGTTTTT-TTTCCGG-TTTG
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AACAAGT-GTTCCCCTGTT-AAAGGA-CGTGGG--TC-AACCGTT-AAA-
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GGG-G--AA--CCGTTTT-TTTATGGG--A--GGC---TT-C--GTTCCG
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TTA-CCTG-TT-AA-GTTTTTTTGGGGTT-TGG-G-CGTAAG-GCT-AAT
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-GGACC-TAATGG-GGCCC-GATTTTGGGTT-TGGGGGAAGCGGA--GAC
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GG-GG-TG-GTGGGTGTAT-GGA-GTC--G-TTAGG-TGGGAAT--T-GG
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TG--T-GG--ATCG-TT-G--T--GGTTTTT-GGT-T-TAGGGGTGGTTT
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--GTGTTTTTT-GTGT-TTG--TT--T
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