Skip Navigation

This Article
Right arrow Full Text (Print 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 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 Strelets, V. B.
Right arrow Articles by Lim, H. A.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Strelets, V. B.
Right arrow Articles by Lim, H. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

Compression of protein sequence databases

Victor B. Strelets and Hwa A. Lim 1

Computational Genetics and Biophysics, Supercomputer Computations Research Institute, Florida State University Tallahassee, FL 32306-4052, USA

1To whom correspondence should be addressed Email: hlim{at}scrtfsu.edu

We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information without extensive decompression of corresponding files. The databank files as well as the interface C-file can be used on both PC-compatibles and UNIX-based computers without any modifications. The interface supports all standard PIR Request Network queries (i.e. gets databank SEQ number by entry; for a defined databank SEQ number, gets specified information like: name, organism(s), keywordfs), sequence, sequence features with coordinates, etc.). In contrast with PIR Request Network, our package allows us to call PIR-contained information directly from the C programs, even on a personal computer not on a network. Our PIR-derived databank, SAGITTARIUS PIR, was implemented in the form of separate file sets. Each file set contains database information of independent types (i.e. sequences, entry indexes, organisms, etc.). On a particular computer, the available configuration of the PIR information (and storage space) can be easily changed as needed by the user without affecting retrievals of other types of stored information. Due to an original alignment-based algorithm, in the compression of protein sequences themselves, our package outperforms the well-known ZIP© file compressor. For PCcompatibles, a dialogue shell is available which supports all standard PIR Request Network queries plus homology searches, alignments, etc

Received on February 16, 1995; accepted on May 23, 1995

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.