The phrase "alignment and extended" is not correct as it lacks clarity and context in written English.
It could be used in a technical or specialized context where "alignment" and "extended" refer to specific concepts or processes, but it needs more information to be meaningful.
Example: "The alignment and extended features of the software improve its overall performance."
Alternatives: "alignment and expansion" or "alignment and enhancement".
In this case, CORAL validates the structural alignment and extends the aligned region.
When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies.
Thus, our results confirm previous findings [19] that topological variation may result from alignment uncertainty and extend this conclusion to the case of uncertainty in the specification of an evolutionary model.
The parameters were set to: amino acid substitution matrix BLOSUM62, a statistical significance threshold of 10 for similarity matches, and costs to open an alignment gap and extend a gap of 11 and 1, respectively.
Blastx parameters were set to: amino acid substitution matrix BLOSUM-62 [ 75], a statistical significance threshold of 10 for database matches [ 76] and costs to open an alignment gap and extend a gap of 11 and 1 respectively.
A given RefSeq was extended with the mRNA sequence that: 1. had at least 300 bp of alignment with the 3' end of the RefSeq; 2. had at least 98% identity with the RefSeq in the region of alignment; and 3. extended the RefSeq the furthest in the 3' direction.
PAGAN can reconstruct ancestral sequences for an existing alignment and then extend that by aligning new sequences against the extant or inferred ancestral sequences.
Aligning Mbre_cRFX1 to human RFX1-3 shows clear alignment for conserved DBD, DD, and extended dimerization domains (B and C domains).
The results showed that many substitutions have occurred in the loop region (middle portion of the alignment in fig. 3) and extended stem regions (left and right ends in fig. 3).
Our algorithm identifies the pair of nodes with the highest alignment score as a seed alignment and gradually extends it using a greedy algorithm.
