To alleviate this difficulty, a number of methods in the literature restricted alignments to specific topologies or network sizes.
We created restricted alignments at the x%-level, i.e. sequences were discarded from each of these alignments so that the minimum percent identity from any sequence to the seed was at least x%.
The introduction of RRBSMAP has significantly increased performance as the program restricts alignment to genomic locations with MspI cut sites (CCGG) (Xi et al., 2012).
In particular, as we show in Supplementary Note 1 in Additional file 1, based on parameter estimates for optical mapping data, restricting alignments to eight missing cuts or five false cuts, consecutively, should retain high sensitivity.
Restricted iterative alignment of each set independently was performed, using an alignment mask on the basal bodies and the needle.
We therefore restricted our alignment to the MACPF domain, the boundaries of which were chosen based on PSI-BLAST results and structural data and then aligned with ClustalW.
To further address the phylogenetic relationship within the obtained haplotypes, we restricted the alignment into three subsets, each comprising 18 haplotypes (10 haplotypes from Cx. annulirostris, 6 from Cx. palpalis and 2 from Cx. sitiens which served as an outgroup).
Conserved stem-loops were also determined by a two-way best alignment between the candidates of both genomes, restricted to alignments with E-value below 1e - 20 and excluding all A. gambiae candidates that overlap known precursors.
The results are difficult to interpret, especially when the retrieved hits share low sequence identity with the starting query or when restricted local alignments identify a single domain in multi-domain protein hits or, finally, when the updating state of protein hits is incomplete and even contradictory making functional transfer difficult [3].
