Sentence examples for remove alignment from inspiring English sources

Manual inspection indicated that these discrepancies were due to GSNAP failing to remove alignment bias when aligning sequences to regions containing more than 5 and as many as 16 heterozygous sites.

Users are provided with parameters to disable the removal of redundant sequences and to remove alignment positions with a high fraction of gaps (insertions or deletions), considered to be of low statistical support.

Geneious was then used to create a consensus sequence for each individual, to align those consensus sequences, and to remove alignment columns containing ambiguous sites and gaps, respectively.

To remove alignment biases at heterozygous variants, AA-ALIGNER uses the allele-aware aligner GSNAP [ 24] which has been previously shown to remove mapping biases using complete genotype information [ 22].

For the purpose of phylogeny reconstruction (see below) the Gblocks program is widely used to remove alignment blocks suspect of low quality, according to various cutoffs on the number of gapped sequences in alignment columns.

Gblocks (version 0.91) [48] with the default settings was used to remove alignment regions that contain gaps or are highly divergent.

The pslCDnaFilter tool was used to remove alignments with less than 200 bp, 98%% identity, or 50%% coverage.

Resulting output was filtered to remove alignments with less than both 50% identity and 50% subject coverage.

The distribution of dN/dS values relative to ClustalW alignment length was evaluated before choosing to remove alignments less than 60% of the total reftig length.

Step 2: Filter the resulting BAM file to: (1) remove alignments with mapq scores of 0; and (2) require a minimum splice junction overhang of 6 bp.

As the sensitivity of RNAz is dependent on base composition and sequence identity, we used a shuffling algorithm developed for ncRNAs [ 59] to remove alignments that also showed a significant RNA structure signal after shuffling.