OHSU

Data Analysis

Base-calling, Editing and Sequence Assembly

do_it_yourself

Highly accurate base-calling is a reliable characteristic of our ABI 3130xL automated fluorescent DNA analyzer. We use the KB basecaller 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 edit the base calls, for A and B mode samples. C and D mode clients must edit their own data. (Our various service levels are described on the DNA Sequencing page.) We highly recommend editing, 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.


Sequence Viewers/Editors

4Peaks or FinchTV for viewing and editing ab1 files.

Several very good sequence viewer/editors are available. 

We especially like 4Peaks for Apple OS X machines.

Geospiza provides a cross-platform program called FinchTV

and Applied Biosystems provides a free viewer/editor for Windows machines called Sequence Scanner.


Trouble-shooting Assistance

Here's an online guide to the ab1 data format and common trouble-shooting issues.