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COW is a global alignment method that cannot short.
In the future, we will discontinue the global alignment method to speed up the tool.
GRAAL (GRAph ALigner) is a global alignment method based solely on the network topology [ 14].
The BLAST-based alignment method produces better separation for certain taxonomy groups than the global alignment method does.
Therefore, we need a more sophisticated global alignment method to standardize the shape of these patterns, before we can proceed further to the local alignment.
We evaluated the performance of SPIC combined with a local or a global alignment method having a function for affine gap penalty, for computing the similarity between two motifs.
Similar(51)
Sequence alignment approaches may be broadly divided into global alignment methods, where sequences are assumed to be homologous and alignable over their entire lengths, and local alignment methods, where only part of each sequence is assumed to be homologous and alignable (Durbin et al., 1998; Gusfield, 1997).
- A new paragraph describing the differences between local and global alignment methods was added.
However, this approach is less useful to evaluate global alignment methods.
We included a small paragraph describing the network alignment problem and the differences between local and global alignment methods.
The performance of other methods shows that classical global alignment methods, MAFFT, ClustalW and ClustalO, struggle in the alignment of short sequence fragments (Fig. 4).
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