Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bonfield, J. K.
Right arrow Articles by Staden, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bonfield, J. K.
Right arrow Articles by Staden, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 1 2002
Pages 3-10
© 2002 Oxford University Press

ZTR: a new format for DNA sequence trace data

James K. Bonfield * and Rodger Staden

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

Received on July 2, 2001 ; revised on September 11, 2001 ; accepted on September 12, 2001

Motivation: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth.

Results: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive.

Availability: Source code is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/io_lib.tar.gz. A complete format description can be found at http://www.mrc-lmb.cam.ac.uk/pubseq/ztr.html. Test data is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/test_data.

Contact: jkb{at}mrc-lmb.cam.ac.uk

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.