Base-calling, Editing and Sequence Assembly
Highly accurate base-calling is a reliable characteristic of our ABI 3730xl automated fluorescent DNA Analyzer. We use the KB base-caller optimized for ABI Prism BigDye Terminator v.3.1. It provides quality scores and can provide ambiguity codes (if requested, the default is A, C, G, T, N).
We highly recommend editing your base calls, especially truncating the low quality reads at the beginning and end of reads, prior to assembly or additional data analysis. This is especially important if you need to design primers for "primer walking" DNA sequencing.
Several very good sequence viewer/editors are available:
- For Apple OS X machines, we recommend CodonCode Aligner
- Geospiza provides a cross-platform program called FinchTV
- Technelysium offers a free trace viewer for simple DNA sequencing project called Chromas for Windows machines (Taylor's favorite)
- Applied Biosystems provides a free viewer/editor for Windows machines called Sequence Scanner