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Based on different alignment rules, several computational models were established with their statistical results compared.
The rapid emergence of high-throughput sequencing techniques has resulted in the development of a variety of short sequence read mappers that are based on different alignment strategies.
Reads were mapped and quantified using the program TMAP (Torrent Mapping Alignment Program; http://mendel.iontorrent.com/ion-docs/Technical-Note---TMAP-Alignment_9012907.html) which is based on different alignment algorithms [ 29– 329.
Moreover, to find potential errors in the alignment, several models based on different alignment versions are usually built and analyzed in terms of parameters such as unfavorable burial of charged residues.
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Only two of the genes, Sphinx1 and Dnr1, were consistently identified in at least two of the three analyses based on different alignments.
Nucleotide positions in the 10-5 map did not correspond to the positions in the QTL-BASE2 and BC1 maps because the SNPs were discovered in different populations and were based on different alignments.
Models based on different target-template alignments have been compared to test QMEANBrane's capability of detecting incorrect alignments, particularly alignment shifts in transmembrane helices.
Until now, a number of network alignment algorithms have been proposed based on different formulations and approaches, many of them focusing on pairwise alignment.
AtFYVE domains can be divided into two distinct groups based on different consensus sequences identified via CLUSTALW multiple sequence alignment (Fig. 5).
The pairwise genomic alignment of mouse/rat available at UCSC is based on different assemblies than the Celera assemblies (Mural et al. 2002) used by Rfam.
> The population structure of O. oeni was investigated by four methods based on different genomic properties: MLST, signature of tetranucleotides, SNP, and whole-genome alignment.
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