Next, the reads at each CAL are further aligned using gapped local alignment to identify the best match.
The main steps in the L_RNA_scaffolder algorithm can be outlined briefly as: (a) Screen optimal alignment to identify 'guide' reads.
The query sequence was used as a reference in the alignment to identify the column position of each possible TRA within the pairwise alignment.
As an example, we have analyzed the tetratricopeptide repeat (TPR) motif, using multiple sequence alignment to identify the significance of each position in the TPR.
We used paired-end alignment to identify structural variation.
We used this alignment to identify amino acid substitutions that correlated with mineralocorticoid sensitivity across GRs.
(C ) Multiple sequence alignment to identify the non-homologous region of BmrD for the homology model.
Then for each query, it performs seeding, filtering and banded alignment to identify the alignments to reference sequences that meet user-defined cutoffs.
Using linker based PCR sequence reads as input iMapper uses a local sequence alignment algorithm to identify a tag sequence derived from the end of the insertional mutagen (Supplementary Material).
The use of some sequence alignment methods to identify a relationship between the target sequence and one or more possible templates is the first step in structure prediction [ 13].
