Compressing DNA sequence databases with coil.

ABSTRACT:

Background

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil.

Results

We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence data

SUBMITTER: White WT 

PROVIDER: S-EPMC2426707 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature