Sentence examples for for local alignment from inspiring English sources

We then used PmHha and LfHhb ar-C sequences and checked for local alignment with Latimeria and rat ar-C sequences.

Five seeding algorithms which have been proposed for local alignment are examined.

For high accuracy, Smith-Waterman (SW) [ 15] is the most widely used algorithm for local alignment.

Two classic algorithms for local alignment are Smith Waterman (Smith and Waterman, 1981) and BLAST (Altschul et al., 1990).

To address these problems, we remap these reads using the BWA-SW algorithm for local alignment [ 22].

Since the seeding algorithm is originally proposed to increase sensitivity for local alignment, the specificity should be considered as well as the sensitivity for the oligonucleotide design problem.

The time to align the homologs to the query might be reduced by using the alignments implied by the families as a starting point to search for local alignments, instead of using BLAST to realign the homologs to the query.

High coverage variation also occurred within the same PCR (coefficient of variation for local alignments of untrimmed reads: 0.46 Roche 454, 0.41 Illumina GA, 0.56 ABI SOLiD, Table S1), with a strong bias for the amplicons ends (Fig. 2), a well-known artifact of UHTS [9].

Parameters used for local alignments were: −evalue 1e-10, −weak_evalue 1e-4, −id 0.9, −weak_id 0.8.

The '–sensitive-local' option was used (which is the default configuration for local alignments. The local alignment mode is beneficial to obtaining good soft clipping results around SVs).

Pairwise alignments were performed using the EMBOSS Needle programme http://www.ebi.ac.uk/Tools/emboss/align/index.html[ 50] for global alignments and the Water programme [ 51] or BLAST2seq for local alignments.