Compressor 4 setup for a 3.4 ghz intel core i7

COMPRESSOR 4 SETUP FOR A 3.4 GHZ INTEL CORE I7 SOFTWARE

We evaluated stand-alone compression tools (rather than libraries), working under Linux OS on a modern workstation PC. Consequently we also did not consider referential compression, but only reference-free compression, which is typically used for such data. Instead we focused on typical FASTA-formatted datasets, which includes individual genomes and single gene sets. In the present study we did not investigate compression of raw sequencing data in FASTQ format, which was previously thoroughly reviewed. We considered the common scenario of archiving, transferring, and working with large datasets of biological sequences. Findings Scope, compressors, and test data The benchmark results are available in the Sequence Compression Benchmark database (SCB database ). Specifically, we focused on the common task of compressing DNA, RNA, and protein sequences, stored in FASTA format, without using reference sequence. Therefore we set out to benchmark all available practically useful compressors on a variety of relevant sequence data. At the same time the field was lacking a thorough investigation of the comparative merits of these compressors for sequence data.

The variety of available specialized and general-purpose compressors is overwhelming. Existing benchmarks with useful visualization such as Squash are limited to general-purpose compressors. In addition, all of these studies provide results in the form of tables, with no graphical outputs, which makes the interpretation difficult. Previous attempts at answering these questions are limited by testing too few compressors and by using restricted test data. However, someone thinking to replace gzip invariably faces the questions, which of the numerous available compressors to choose? And will the resulting gains even be worth the trouble of switching? Through all these years the amount of stored sequence data kept growing steadily, increasing the load on database operators, users, storage systems, and network infrastructure. This incredible longevity of the 27-year-old compressor probably owes to multiple factors, including conservatism of database operators, wide availability of gzip, and its generally acceptable performance. However, despite this activity, currently nearly all databases universally depend on gzip for compressing FASTA-formatted sequence data.

COMPRESSOR 4 SETUP FOR A 3.4 GHZ INTEL CORE I7 SOFTWARE

A lively field emerged that produced a stream of methods, algorithms, and software tools for sequence compression. Biological sequence compression was first proposed in 1986, and the first practical compressor was made in 1993. Molecular sequence databases store and distribute DNA, RNA, and protein sequences as compressed FASTA-formatted files.

Compressor 4 setup for a 3.4 ghz intel core i7