Similarly, candidate SNP containing regions of the reference genome should be supported by multiple sequences, such as transcript sequences and/or sequences from more than one BAC clone to avoid any possible sequencing errors (Additional file 4).
There are many algorithms and tools available for the basic problem of aligning multiple sequences, such as ClustalW [ 23], MUSCLE [ 24, 25], BLAST [ 26], and the T-Coffee suite [ 27].
Such tools are used for discovery of short elements in a single or multiple sequence contexts, such as transcription factor binding sites.
Nevertheless, lhRNAs in combination with other multiple RNAi effector sequences, such as Pol II-expressed multiple miRNA precursors [14], [18], [19], are likely to provide an effective means of targeting rapidly evolving sequences such as HIV-1.
Typically, most authors compare their methods against a handful of other methods for a dataset, or in some cases against collections of multiple sequence alignments, such as the Pfam database [16].
Combinational interactions between multiple sequence motifs such as two upstream activating sequences UAS1 (−295 to −109) and UAS2 (−468 to −391) affected the spatial and temporal regulation of the promoter.
Tools for multiple sequence alignments such as ClustalW (Thompson et al., 1994) are readily available and thus, structure prediction from an alignment is a tempting approach [e.g. RNAalifold (Hofacker et al., 2002)].
The k-mers counting method was implemented in some important multiple sequences alignment tools, such as MAFFT [ 6, 7] and MUSCLE [ 1], and to the extent of our knowledge there is no other work in the literature that has developed and tested a parallel approach, specifically of this method.
While our results (Table 2) coincide with previous findings that HMM-based predictors outperform other predictor types (i.e. NNs and SVMs), we consider that β-barrel's topology predictors could be more useful tools if they allowed for submission of multiple sequences and/or provided precomputed runs, such as commonly studied genomes such as E. coli.
This enables the use of proportionately larger hash tables and thereby enables fast indexing of larger sequences such as multiple whole mammalian genomes.
Bacterial genomes include several repetitive sequences such as multiple copies of ribosomal RNA operons and insertion sequences or transposases.
