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Sequence traces were assembled and analyzed using a modified version of the PolyPhred software package.
Traces were assembled in CodonCode 2.0.6 (CodonCode Corporation, Dedham, MA).
The traces were assembled using Phrap and Consed [ 41].
The traces were assembled into bidirectional contigs, primer sequences were removed, and all ambiguous base calls were checked manually.
Sequence traces were assembled and analyzed to identify potential genomic alterations using the Mutation Surveyor software package (SoftGenetics, LLC, State College, PA, USA).
Assemblies were analyzed both manually and based upon BAC-specific tags to determine that sequence traces were assembled into the correct BAC contig.
Similar(54)
These unique-hit redundant traces are assembled into a larger DNA contig using the CAP3 program [ 44].
With this aim in mind, the unitigger error rate, which specifies the threshold of similarity at which two traces are assembled, was adjusted over a range of values.
Sanger trace files were assembled using the Staden sequence assembly package [ 71], and compared to the Illumina derived sequence using the MEGA5 alignment tools [ 72].
Trace files were assembled into contigs with the SeqMan application in the DNASTAR software package.
Trace files were assembled using the Staden package ver. 1.6 (Staden 1996) and Sequencher (Gene Codes Corporation, Ann Arbor, MI).
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