In addition to alignment, other steps are equally important to get high-quality and analyzable data for downstream analyses.
In addition to alignment uncertainty, saturation at silent sites (dS) may also bias the inference of positive selection (Smith and Smith 1996).
The two ribosomal RNA genes (12S and 16S) were annotated as the sequences between flanking tRNA Phe, Val and LeuUUR in addition to alignment using previously determined myctophid RNA genes [ 33].
In addition to alignments to Core Eukaryotic Genes, BUSCO, tick, and fruit fly, we also aligned our assembled transcripts to proteins in UniProtKB (August 2012 release) and NCBI's nr database (August 2012) using BLASTX with E-score cutoffs of 1e-5.
In addition to alignments to the genome, reads were assembled de novo using a hybrid assembly technique.
In addition to alignments to the Glyma models, candidate soybean ESTs corresponding to the tags were used for further verification of the DGE differentially expressed tags referenced in the Table 1.
In addition to alignments between GLEAN predictions and RefSeq genes and peptides, we considered numbers of gene models, total numbers of coding nucleotides, average coding sequence lengths, and numbers of splits and merges compared to RefSeq.
In this study, we use this idea to compare the most widely-used methods for pairwise structural alignment, in addition to considering alignment accuracy relative to other annotation sources: DSSP structural classes (Kabsch and Sander, 1983) and solvent accessibilities.
In addition to tabulated alignments, graphic alignments were generated and grouped in three tiers: 1) viral gene annotation, 2) viral transcriptomes, and 3) viral proteomes (legends of Figure 1 and Figure 2).
In addition to the alignment, tools exist to improve the quality of an existing alignment, for example, with local indel realignment.
In addition to gapped alignment in the Bowtie2 step, TopHat2 also allows indels in the spliced alignment detection step.
