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Due to recent progress of pyrosequencing and other 'next-generation sequencing' techniques [70], the analysis of a considerably increased number of sequences is becoming affordable.
The increased number of sequences found in pools confirmed false negative results obtained after the initial stringent analysis, which was indicated by PCR screening (see above).
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Despite the numerous advantages of using next generation sequencing, 454 amplicon sequencing is particularly prone to sequencing errors such as homopolymers [ 40, 41] resulting in an increased frequency of indels [ 29] or to increased number of sequenced chimeras [ 34].
An increased number of sequenced genomes led to a revised view of the origin of metazoan life.
An increased number of sequenced ESTs frequently reveal additional alternative splicing events because more and more rare splicing variants from genes with low expression become sequenced.
In experiments with high specificity, the majority of sequence tags are derived from the real modified sites, while in experiments with high level of noise, there are increased number of sequence tags derived from other sites.
The rapidly increasing number of sequences entering the genome databanks has called for the development of automated analysis methods.
Additionally, the increasing number of sequences in the biological databases is perceived as one of the upcoming challenges for alignment methods in the nearest future.
Given the increasing number of sequences available, analyzing new haplotypes together with all previously published sequences will be time consuming and will require huge computational resources.
Although obtaining a best-fit ML tree with an increasing number of sequences and sequence length is computationally intractable (NP-hard), a ML-based method can provide statistical comparability of the fitness of substitution models [6], [7].
It takes advantage of the increasing number of sequences with an experimentally characterized homolog in the PDB database.
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