Sentence examples for alignment methods such from inspiring English sources

For instance, the latest version of T-Coffee (Version 6.00) is able to combine up to 15 different alignment methods, including pair-wise structural aligners, regular multiple sequence alignment methods and even RNA alignment methods such as Consan (Dowell and Eddy, 2006).

On the other hand, the proposed method has also been compared with recently proposed state-of-the-art range-bin alignment methods, such as the global range alignment algorithm and the minimum entropy-based approach.

Further, the extent of repeat was verified through structural alignment methods such as DALI [18], LSQMAN [19] and also through the examination of domain topologies with HERA [20].

As a hybrid, SARST was almost as precise as conventional PSC methods like CE in structural similarity searches while at the same time it possessed some properties of sequence alignment methods such as the high running speed [34].

It may seem peculiar to use a de novo assembler to help validate single-base changes in genomes, especially now that fast and large-scale read alignment methods, such as bwa [17], exist.

Detection of very distant homologs is often possible by using PSSM-based sequence alignment methods such as PSI-BLAST[4] or hidden Markov models[3], [15] because a PSSM is specific to a particular protein family so that some family-specific features can be exploited.

In practice, users will most likely use a more sophisticated alignment method, such as FUGUE (Shi et al., 2001), yielding somewhat better accuracies.

Although CE outperforms writher in general, this result shows that writher has potential to improve sensitivity of a full alignment method such as CE in a local alignment task.

These methods are categorized into two general groups (Hudson and Quail 2003; van Hijum et al. 2009): alignment (probabilistic) methods, such as MEME (Bailey and Elkan 1994), DMBP (Huang et al. 2005), AlignACE (Hughes et al. 2000), and Motif Sampler (Thijs et al. 2001), and enumerative methods (Hudson and Quail 2003; van Hijum et al. 2009).

A discussion of 'forward' scores, which sum over all possible alignments, versus methods such as Smith-Waterman (and also BLAST), which consider only the highest scoring alignment, would not have been out of place during the early years of GIW.

Even though Sailfish is substantially faster than alternative alignment-dependent methods such as Cufflinks, using all k-mers in the transcriptome quantification impedes the scalability of the method.