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File Formats

The following are links to the new manual. Hence the previous and next links from there point to other pages within the manual rather than back to here.

SCF format files are used to store data from DNA sequencing instruments. Each file contains the data for a single reading and includes: its called sequence, its trace sample points, and numerical estimates of the accuracy of each base. The format is machine independent and was first described in Dear, S and Staden, R. "A standard file format for data from DNA sequencing instruments", DNA Sequence 3, 107-110, (1992).

ZTR is designed to be the successor of SCF. It stores the same binary trace data as SCF, but is more widely extensible and is substantially smaller due to the use of internal compression routines.

Experiment File
Experiment files contain gel readings plus information about them, and are used during the processing of the sequence. They are used to carry data between programs: they provide input to the programs and programs may in turn add to or modify them. When the experiment file for a reading reaches the assembly program it should be carrying all the data needed for its subsequent processing. The assembly program will copy what it needs into the assembly database. The files are based on EMBL sequence entries and, if required, can be read as such by programs like Spin.

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This page is maintained by staden-package. Last modified November 27th 1995.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/formats.html