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Simultaneous sequence analysis of all organisms in filtered samples from the Sargasso Sea indicates the presence of over 1800 species, with unexpectedly large microbial diversity.
Clearly, it is possible to have a single probabilistic methodology for finding similarities based on sequence, structure or simultaneous sequence and structure.
For this reason, the sequencing of bread wheat (cultivar Chinese Spring) by the International Wheat Genome Sequencing Consortium [ 6, 7] is being carried out on individual flow-sorted chromosomes [ 8, 9] to (at least) avoid the difficulty of simultaneous sequence assembly of closely related homoeologs.
In the current study, simultaneous sequence comparisons of the entire protein-coding portions of the genomes of four fish model species (Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oryzias latipes) with the human outgroup genome were conducted in order to study the evolutionary extent of sequence conservation and divergence in duplicated fish genes.
Among other things refinements could include additional exploratory analyses of data signal and conflict, separate analyses of stems and loops for the ribosomal genes, the use of different or simultaneous sequence alignments, incorporation of the very latest morphological evidence [ 56], or likelihood testing of alternative phylogenetic topologies.
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We evaluated the strength of Next Gene-ration Sequencing (NGS) technologies to fulfill these criteria through simultaneous sequencing of the major known causative genes described as responsible for these phenotypes.
The Ion Torrent PGM™ next generation sequencing platform allows for the simultaneous sequencing of up to 96 barcoded samples in a single two to four hour run, providing a method to process a large number of gene sequences in significantly less time than traditional sequencing.
Barcoded genomic libraries were prepared from Castor DNA as described previously [41], [43], allowing the simultaneous sequencing of different samples on the same 454 lane.
However, the recent introduction of deep sequencing technology, enabling the simultaneous sequencing of up to millions of DNA or RNA molecules, has provided another option for the discovery of novel miRNAs that may have eluded previous efforts [13].
Currently, the method provides a means for the simultaneous sequencing, generation of single molecule sequences, and assignment of short (∼120 bp) from homologous PCR products obtained from multiple individuals.
The use of a bar-coding strategy [11], in which unique sequence identifiers to PCR primers allowed for pooling and simultaneous sequencing of a large number of distinct samples in a single pyrosequencing run followed by bioinformatic sorting of sequences, allowed for comparative diversity studies to be conducted across hundreds of samples simultaneously in a single sequencing run.
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