Compression of protein sequence databases

VB Strelets, HA Lim - Bioinformatics, 1995 - academic.oup.com
VB Strelets, HA Lim
Bioinformatics, 1995academic.oup.com
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 …
Abstract
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
Oxford University Press
Showing the best result for this search. See all results