Sentence examples for to refine the alignment from inspiring English sources

In summary, our method takes advantage of (i) second-order Gaussian derivatives detectors for localizing the markers [21], (ii) a cluster analysis to identify them throughout a series and (iii) iterative procedures to refine the alignment process.

MatchedIonsFinder was used to refine the alignment results.

We just used our pairwise potential to refine the alignment generated by local alignment potential as follows.

ScanIndel employs BLAT to refine the alignment of split reads, since it is known that BLAT is much better than short read aligners at mapping sequences with gaps.

The sequences were aligned on the genome using initially a blast program [ 58] to quickly identify the similarity regions and Exonerate [ 59] software to refine the alignment.

Gblocks (Castresana 2000) was used to refine the alignment (supplementary file S2, Supplementary Material online) and a maximum-likelihood tree was calculated using 1,000 full bootstrap replicates with RAxML v7.7.6 (Stamatakis 2006) using the PROTGAMMAWAGF substitution matrix.

The de novo transcript assembly was input into PASA [ 40] to refine the alignment-based gene models with mRNA evidence.

GATK6 was used to refine the alignments near insertion/deletion (indel) sites.

The PRRN program was then used to refine the alignments to improve the precision of those with lower sequence similarities.

Once the sequences of the 90e/genomic contig pairs were retrieved, exonerate[ 62] was used to refine the alignments over the splice sites (using as parameters model = est2genome and bestn = 10).

To further refine the alignment, the web-based Mulan program was utilized, which performs a full local multi-sequence alignment that can account for evolutionary reshuffling and inversions using the threaded blockset aligner program [ 87, 88].