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DNA sequence traces were edited with Chromas 2.3 (http://www.technelysium.com.au).au
The program analyses each trace and adjusts it in relation to the peak heights of upstream/downstream nucleotides, allowing rapid batch wise analysis of DNA sequence traces for estimation of the relative proportions of two QSVs at a given site.
(C ) DNA sequence traces for four alleles of sbr.
We have used iMapper to analyze up to 20 000 DNA sequence traces.
The ESTs were further processed with Phred program [ 9] for base calling DNA sequence traces.
Automated contig-assembly and base-calling of DNA sequence traces were performed by using the EWGLI sequence quality tool (16 ).
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DNA sequence trace files were aligned with the program Sequencher™ (Gene Codes Corp ,MI), and analyzed for levels of sequence divergence as described below.
The Read.pm object describes a DNA sequence trace and includes methods for data import from a variety of formats.
Novel alleles and STs (allelic profiles) were assigned designations by the database curator following submission of DNA sequence trace chromatograms (http://www.mlst.net).net
ESTPiper incorporates the Phred program [ 7] for base calling with quality scores, which is the de facto standard program for converting DNA sequence trace files (i.e., chromatograms) generated by the Sanger method into nucleotide sequences.
Exon 3a was aligned with the mouse genomic Txnrd1 DNA sequence (Trace Archive 18378992) to confirm a consensus splice sequence at the 5' splice donor site to form the intron between exon 3a and 3b.
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