Sentence examples for alignment-based method from inspiring English sources

Also, its comparison against an alignment-based method, based on which almost all conclusions of its superiority were drawn, is inappropriate, as argued above.

We developed an alignment-based method that allows to quantify the similarity of ncRNAs solely based on primary deep sequencing data by considering the position and length-dependent patterns of reads aligned to short intervals on the genome.

Many HLA typing efforts have been made by mining NGS data, including the alignment-based method that relies on counting the number of short reads aligned to each specific allele [ 8], the assembly- and scoring-based method that takes into account good quality contigs and their scores for each candidate HLA allele [ 9].

The alignment-based method is in agreement with antiSMASH on this cluster definition (Additional file 6).

AntiSMASH agrees with the alignment-based method on this definition of SC3 (Additional file 4).

A quantitative alignment-based method, RIPCAL [ 34], was used to search for evidence for RIP in E. pusillum genome.

Alignment-based methods have been in use ever since Woese first demonstrated rRNA sequence based phylogenetic trees [12].

Therefore, the main challenge for the alignment-based methods was to devise ways of combining multiple hits or identified domains into a single prediction score.

The proposed method was tested by phylogenetic analysis, and its performance was further compared with alignment-based methods.

Alignment-based methods relying on molecular superposition retain almost all of the shape information of a molecule but do not encode shape in a numerical form.

The unprecedentedly wide scope of ligand definition and large-scale topological similarity mapping can provide very robust tools, of performance unmatched by the present alignment-based methods.