Sentence examples for in alignment mode from inspiring English sources

Homology modeling was done in alignment mode through SWISS-MODEL (http://swissmodel.expasy.org/).org/

Let H S A m (T, S) denote the optimal alignment cost of trees T and S in alignment mode m, where m is one of the following modes: Rooted-Ordered, Rooted-Unordered, Unrooted-Ordered or Unrooted-Unordered.

Let R e l S c o r e m (T, S) denote the relative score of T and S in alignment mode m, given by [ 48]: (8) RelScor e m (T, S ) = 2 HS A m (T, S ) HS A m (T, T ) + HS A m (S, S ).

For long reads with lower quality at the 3' end, or data where some tiles have low sequence quality in several cycles, Bowtie2 in local alignment mode will achieve higher mappability but requires slightly longer CPU times.

The combined dataset comprising a total of 165 sequences was aligned with POA (version 2) in progressive alignment mode [62].

The 76 bp pair-end reads were filtered for quality as described above and aligned to genomic PST assemblies using Bowtie (version 0.12.7 [ 51]) in global alignment mode allowing a maximum of two mismatches (parameters: -v 2 --best -k 1).

DNA sequences of AVD, AVR2, AVR4, AVR6, AVR-A, AVR-B, AVR-C and BBP-A and BBP-B were aligned exon by exon and intron by intron using Clustal X in multiple alignment mode with default values for both pairwise and multiple alignment parameters.

The decision tree-based state clustering tool of HTK produced 858 tied states, and evaluating the phone models in forced alignment mode yielded the training targets for each frame of speech.

For individual repeat alignments HHpred submissions were made without an additional PSI-BLAST step and in global alignment mode.

Alignment to the reference was done using bowtie2 2.1.0 in local alignment mode.

Then the CM is applied in local alignment mode to validate the candidate.