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Next-generation sequencing technologies produce unprecedented amounts of data, leading to completely new research fields. One of these is metagenomics, the study of large-size DNA samples containing a multitude of diverse organisms. A key problem in metagenomics is to functionally and taxonomically classify the sequenced DNA, to which end the well-known BLAST program is usually used.
But BLAST has dramatic resource requirements at metagenomic scales of data, imposing a high financial or technical burden on the researcher. Multiple attempts have been made to overcome these limitations and present a viable alternative to BLAST. Supplementary data are available at Bioinformatics online. Next-generation sequencing has opened the door to a multitude of possible research fields, among them metagenomics.
Usually it is attempted to either assemble the genomes Rene bazinet speed dating the organisms contained in the sample or to determine its taxonomic content, i.
This means assigning a read to a known, usually protein-coding and annotated, subject sequence to identify the encoded function, the organisms present in the sample or identify the closest relative. Bazinet and Cummings give an overview of the various programs that have been developed to address this problem. Another metagenomic study Mackelprang et al.
Hence, since some time there is an effort to replace the BLAST suite by algorithms and tools that are much faster while not sacrificing too much accuracy. That means the tools aim at finding the same alignment locations as BLAST and possibly an alignment
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