Sentence examples for converted to alignment from inspiring English sources

The resulting alignment file is converted to alignment coordinates and sorted by reference ID using MUMmer's "show-coords" function.

Then, ReXSpecies aligns the transcription factor binding site predictions such that their sequence coordinates are converted to alignment coordinates considering gaps, which have been introduced by the alignment tool, as described in [ 7].

For each poplar clone, the paired-end reads were aligned separately using the aln command with default settings, and then converted to alignments in the SAM format in pairs via the sampe command.

For each pair of homologs, their protein sequences were aligned with CLUSTALW [ 53] and their protein alignment converted to DNA alignment with PAL2NAL [ 54].

Alignments were converted to sequence alignment map format followed by binary alignment map, sorted and indexed (Samtools version 0.1.19).

The resulting sequence alignment map (SAM) files were converted to binary alignment map (BAM) files, and subsequently sorted via SAMtools.

Protein alignments were converted to DNA alignments.

Protein-based alignments were converted to nucleotide alignments by using RevTrans [ 71].

To map the raw 44 or 75 nt pair-ended BS-Seq reads, the original reads were computationally converted to the alignment forms with the following steps: 1) observed cytosines on the forward read of each read pair were in silico replaced by thymines; 2) observed guanines on the reverse read of each read pair were in silico replaced by adenosines.

The amino acid alignments were then converted to nucleotide alignments using the PAL2NAL program [ 46].

The protein alignments of bik2– bik6 were converted to nucleotide alignments using the PAL2NAL script (Suyama et al. 2006), this time including only genes from F. fujikuroi, F. oxysporum, F. verticillioides, two B. cinerea strains (T4 and B05.10), and the nearest outgroup from the RAxML amino acid analyses.