Abstract
A “sequence format” is a punctuation style, or defined layout of text, within a computer file that separates a sequence from everything else. It allows computer programs that “understand” the format to distinguish between the sequence and any reference documentation also in the file. Some format definitions extend to the documentation itself (i.e., most database formats), allowing some software to locate specific reference information (e.g., authors, journals, species classification, coding regions).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Stoehr, P. J. and Cameron, G. N. (1991) The EMBL data library. Nucleic Acids Rex 19, 2227–2230.
Burks, C., Cassidy, M., Cinkosky, M. J., Cumella, K. E., Gilna, P., Hayden, J. E.-D., Keen, G. M., Kelley, T. A., Kelly, M., Krrstofferson, D., and Ryals, J. (1991) GenBank. Nucleic Acids Res. 19, 2221–2225.
Devereux, J., Haeberli, P., and Smithies, 0. (1984) A comprehensive set of sequence analysis programs for the VAX Nucleic Acids Res. 12, 387–395.
Orcutt, B. C, George D. G, Fredrickson, J. A., and Dayhoff, M. 0. (1982) Nucleic acid sequence database computer system. Nucleic Aczds Res. 10, 157–174.
Orcutt, B. C., George D. G., and Dayhoff, M. 0. (1983) Protein and nucleic acid sequence database computer systems. Ann. Rev. Biophys. Bioeng. 12, 419–441.
Hunt, L. T. (1990) in Protein Identification Resource Newsletter, vol.9, May. National Biomedical Research Foundation, Washington, DC.
Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444–2448.
Staden, R. (1986) The current status and portability of our sequence handling software. Nucleic Acids Res. 14(1).
Gilbert, D. G. (1989) ReadSeq, C and Pascal routmes for convertmg among nucleic acid & protein sequence file formats, suitable for various computers. Published electronically on the Internet, available via anonymous ftp to ftp.bio.indiana.edu
Barker, W. C., George, D. G., Hunt, L. T., and Garavelli, J. S. (1991) The PIR protein sequence database. Nucleic Acids Res. 19, 2231–2236.
Bairoch A. and Boeckmann B. (1991) The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 19, 2247–2249.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
O’Donnell, C. (1994). Converting Between Sequence Formats. In: Griffin, A.M., Griffin, H.G. (eds) Computer Analysis of Sequence Data. Methods in Molecular Biology, vol 24. Humana Press. https://doi.org/10.1385/0-89603-246-9:333
Download citation
DOI: https://doi.org/10.1385/0-89603-246-9:333
Publisher Name: Humana Press
Print ISBN: 978-0-89603-246-0
Online ISBN: 978-1-59259-511-2
eBook Packages: Springer Protocols