Next-generation, massively-parallel sequencing technologies have transformed the landscape of genetics through their ability to produce giga-bases of sequence information in a single run.
High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total.
These platforms can analyze tens to hundreds of millions of DNA fragments simultaneously, generate giga-bases of sequence information from a single run, and have revolutionized SAGE and cDNA sequencing technology [ 11, 12].
High-throughput short-read technologies have revolutionized DNA sequencing by drastically reducing the cost per base of sequencing information.
Community DNA isolated from a production-scale biogas plant fed with maize silage, green rye and low amounts of chicken manure was sequenced on the Genome Sequencer FLX platform which resulted in 142 million base pairs of sequence information.
More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome.
Degenerate and specific PCR primers were designed for the detection of chloroethene reductive dehalogenases (CE-RDase), the key enzymes of chloroethene dehalorespiration, based on sequence information of three CE-RDases and three chlorophenol (CP) RDases.
Another class of applications is the prediction of molecule properties based on sequence information, such as the prediction of replication capacity based on HIV-1 sequence variation [ 74].
Recently, support vector machines have been used to predict crystallization propensity of proteins based on sequence information [ 2, 4, 10, 36].
Moreover, slight variation in these parameters, or the use of analyses based on sequence information content and base composition (which also distinguish P- from R-segments) gave essentially similar results (not shown).
