Sentence examples for paired alignments from inspiring English sources

Generation and analysis of paired alignments within LTR retrotransposon families revealed numerous retroelements containing clusters of G to A mutations, signs of DNA editing by A3 (2,459 elements, 23,853 edited nucleotides).

Both sets of paired alignments had no gaps.

A mixed model was used, which allowed unpaired alignments when paired alignments were not possible.

Scores of paired alignments were compared to scores and standard deviation for 50 randomized sequences with base composition-preserved.

For paired-end reads, we set the maximum fragment size at 1000 (-X 1000) and used the -y option to maximize Bowtie's sensitivity to find paired alignments.

From the.bam files, we extracted properly paired alignments using SAMtools (Li et al. 2009) with the command "samtools view -f 3".

The percent amino acid sequence divergence was calculated from the output of the paired alignment.

We refer to such a multiple sequence alignment of paired sequences as a paired alignment.

Both sequences were extracted using an ad hoc Perl script (homemade) formed for each paired alignment.

Novoalign (www.novocraft.com) computes a similar mapping quality for each paired alignment, but it relies on the user to provide the fragment size distribution.

The paired alignment is then filtered to reduce redundancy to 90% sequence identity and to remove positions that have more than 75% gaps.