Sentence examples for incorporated into the alignment from inspiring English sources
Secondary structure prediction was incorporated into the alignment for Phyre2 (and all of the other modeling servers used for comparison including Swiss-Model and Tasser).
The hypothesized single nucleotide deletion in the C-terminus of eu AP3 lineage members was incorporated into the alignment (see Additional file 3 for complete alignment in NEXUS format).
Following these observations, we finally demonstrate that biologically meaningful alignments can be produced by both programs if additional information regarding these repeats or other forms of "expert knowledge" are incorporated into the alignment procedure.
These sequences were retrieved, and incorporated into the alignment with the true 4.1 proteins.
Assemblies showed no evidence of gaps in coverage that could be indicative of linear numts incorporating into the alignment (Sorenson and Quinn 1998; Thalmann et al. 2004), nor were there anomalously divergent sperm whale mitogenome regions or premature stop codons that would indicate the incorporation of ancient pseudogenes (Sorenson and Quinn 1998; Nabholz et al. 2010).
Moreover, the resulting alignment retains biological knowledge that was incorporated into the existing alignment.
Because only a subset of the T. dalmanni EST consensus sequences have homologous sequence in D. melanogaster that is incorporated into the Blast alignment, this search resulted in fewer total polyglutamine repeats than were identified in the search of the entire EST database.
The treated amphioxus data were subsequently incorporated into the protein family alignments used for the initial Blast analysis of the amphioxus genome.
One reason progressive methods are so strongly dependent on a high-quality initial alignment is the fact that these alignments are always incorporated into the final result — that is, once a sequence has been aligned into the MSA, its alignment is not considered further.
This algorithm was incorporated into the MAFFT suite of multiple sequence alignment programs [ 14].
Through the use of the PASA pipeline, the majority of EST and FL-cDNA alignments were incorporated into the Arabidopsis gene annotations.
