Moreover, some of them make possible to analyse and model RNA-Seq protocols.
See also Genetic Simulation Resources and some discussion about simulation at Biostars.
The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface.
In this case reads are assembled directly in transcripts.
The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples.
Some software are also designed to study the variability of genetic expression between samples (differential expression).
Quantitative and differential studies are largely determined by the quality of reads alignment and accuracy of isoforms reconstruction.
Furthermore, even the species under investigation and the biological context of the samples are able to influence the results and introduce some kind of bias.
Many sources of bias were already reported – GC content and PCR enrichment, Recent sequencing technologies normally require DNA samples to be amplified via polymerase chain reaction (PCR).Yet, our understanding of the microbial ecology of drinking water distribution systems (DWDS) is limited, partly as these environments are not easily accessible and because they have traditionally been considered as challenging environments for microbial life when compared with other aquatic ecosystems.However, available scientific literature fuelled by the application of recent advances in molecular-based methods to drinking water ecosystem indicates that DWDS are diverse microbial ecosystems, with high bacterial and fungal abundance, but where a variety of microbial life from viruses to protozoa can be found ().Several studies are available comparing differential expression methods.Genome arrangements result of diseases like cancer can produce aberrant genetic modifications like fusions or translocations.Some of this data comes from other expression methods like expressed sequence tags (EST).