Sentence examples for a native alignment from inspiring English sources

The idea is to test whether adding more sequences to a native alignment can help homology detection.

We demonstrate that adding reconstructed ancestral sequences to a native alignment improves the detection of homologs in database searches.

The third method (conservation difference or CD) is based on the conservation differences between a native alignment and an alignment derived from the Z-score sequence design [ 21].

Adding non-native sequences to the native alignment results in a change of sequence profile for PSI-BLAST searches.

Since the pairwise potential in the Z-score design tends to weaken the conservation caused by function, functionally conserved sites tend to have a large conservation difference between the native alignment and the alignment of designed sequences.

In the third case, we shuffled the native alignment at each position while keeping the gap pattern as in the native alignment.

However, sequences generated by shuffling each position of the native alignment have the same conservation properties as the native alignment, and the "SHUFFLE" method detects a total of 74 new homologs.

The benchmark experiment was PSI-BLAST seeded with the native alignment (N sequences).

After shuffling, we added N-1 sequences resulted from the shuffling to the native alignment.

Four types of combined alignments were generated, adding different sets of N-1 sequences to the native alignment.

In the fourth case, N-1 random sequences were generated with the overall amino acid frequencies of the native alignment.