Sentence examples for used for profile alignment from inspiring English sources

ClustalX v1.83 was used for profile alignment and to manage aligned sequences (Thompson et al. 1994).

For profile alignment, we used HMMER 2.3.2 (Eddy, 2008) to build a profile HMM from the training alignment subset with hmmbuild using the -f option to build local alignment models, and aligned each test fragment to the profile (thereby adding it to the multiple alignment with the training sequences) with hmmalign using default parameters.

The use of guide trees for this step highlights the need for available definitive bifurcating trees for profile alignments, especially broadly sampled trees.

Aligned protein blocks for each domain were then combined using a profile alignment in ClustalW [9].

To align query sequences to these pre-existing alignments, we used the CLUSTALW profile alignment algorithm.

We have used profile alignment to avoid the challenges of multiple sequence alignment on large families.

Two diverse sequences from the remote member family, the 3-hydroxyisobutyryl-CoA hydrolases, for which no experimentally determined structure is available were themselves aligned to the structure-based alignment using the profile alignment option in MUSCLE[43].

Alignments were generated individually for each Osiris group, including all Osiris sequences at once, and using the profile alignment option.

The MAFFT-profile alignment option was used for constructing a combined profile alignment from the above mentioned alignments.

The full length cDNA alignment and exon 2 DNA alignments were merged using the profile alignment facility within the Clustalw program to create a 34 by 759bp alignment.

DNA Multiple alignments were produced using the CLUSTALW program using the profile alignment option to merge alignments of the long (fill length) and short (exon 2 only) sequences.