Next, a subroutine GREEDY_ALIGNMENT (A, F') takes an alignment A and a set of fragments F' as arguments and returns a new alignment A' ⊃ A by adding fragments from the set F' in a 'directly' greedy fashion.
For each of the alignments, a set of all Micromonas (Prasinophyceae) sequences available in the ITS2 database was used as the outgroup.
After manual review of all of the global nucleotide and protein alignments, a set of 1227 non-redundant feline sequences were selected as high confidence, high quality feline sequences.
For measuring the alignment accuracy, we aligned a set of reads against both its reference BAC, RefBAC and an extra sequence from a different source, RefEX.
A HAL graph, therefore, decomposes a multiple alignment into a set of pairwise alignments, which are represented as breakpoint graphs.
Even if we solved partially this problem by automatically rejecting highly divergent or missannoted sequences and if we choose one of the best alignment software, a set of the alignments generated will be inconsistent.
An idealized WD repeat was designed from a structure-based sequence alignment with a set of structural guidelines.
In the alignment stage, a set of N initial substructure pairs is found using a novel approach.
The core algorithm is based on the alignment of a set of optimal atom triads followed by volume overlap scoring.
