Sentence examples for trimming alignment from inspiring English sources

The application-specific alignment features were considered as follows: multithread, gapped alignment analysis, paired-end alignment analysis, trimming alignment analysis, and bisulfite alignment analysis.

We performed read mapping for the entire set using the final pre-submission version of the Vervet Reference Genome, consisting of 2,199 scaffolds, and followed the procedures described above for read trimming, alignment, and marking of duplicates.

The removal of positions with gaps in more than 50% of the sequences resulted in a trimmed alignment of 31,123 amino acid positions, which was subsequently used for Maximum Likelihood (ML) pylogenetic reconstruction, using a 4-rates gamma distribution model.

A second pass of variant calling and coverage estimation was performed on the trimmed alignment files.

The trimmed alignment is presented in supplementary datafile S2 (fasta), Supplementary Material online.

This phylogenetic tree was built on the trimmed alignment described above.

Amino acid sequences with gaps in greater than 25% of the sites of the trimmed alignment were removed.

The trimmed alignment (after removing indels) was 476-bp long and yielded 17 distinct haplotypes defined by 17 variable sites.

Following the alignment of the vertebrate TAARs, we manually removed long overhangs introduced by the out-groups and used this trimmed alignment for the phylogenetic analysis (File S2).

The trees produced with this trimmed alignment were compared with the set of trees produced from the alignment of the mouse sequences to their respective full-length proteins.

The conservation threshold corresponds to the minimum percentage of columns, from the original alignment, which the user wants to include in the trimmed alignment.