Sentence examples for length of alignment from inspiring English sources

- Length of alignment denotes number of aligned residues The table shows the alignment accuracy by RMSD, the length of alignment, and coverage, which is the fraction of the aligned residues in the target protein.

Sn1 is the raw score S normalized by the length of alignment including gaps between the query and template sequences.

All subsequent reads were considered to be valid DNA or valid putative mRNA derived sequences and were annotated against the SEED database using MG-RAST (e-value <1×10−3; minimum length of alignment of 50 bp; minimum sequence nucleotide identity of 50%; [30]) to produce an abundance matrix of functional genes and protein-derived predicted taxonomies across the DNA and mRNA samples.

This optimization is based on two contradictory criteria including the length of alignment and RMSD.

Using only ECR blocks exhibiting direct phylogenetic relatedness, we quantified the total length of alignment across each contig, the total length of alignment not including species-specific insertions, and the percent identity of the entire aligned region.

The high efficiency of the method is yielded by the high length of alignment with a relatively low RMSD.

In general, the length of alignments increases with decreasing gap penalty, however also the number of correctly assigned ortholog pairs rises up to 38% of all human-zebrafish EnsEMBL orthologs (Figure S4).

Sequence identity was calculated over the full length of alignments generated using MUSCLE.

A partial estimate of the impact on more distantly related sequence comparisons is the increased number of contigs for which no cross-species alignments were found and the reduction in average length of alignments.

In practice, we have found that better resolution can be achieved using networks of full-length sequences, as the greater variation in lengths of alignment and corresponding similarity scores allows a more nuanced discrimination between different groups of proteins.

For each proportion of characters with heterogeneous composition (i.e. 0%, 10%,..., 50% of the length of the alignment), 500 four-sequence alignments were generated following this procedure.