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In order to reduce signaling overhead for index of reference signal sequences, the n cs UE is limited to take among 12 candidate values ranging from 0 to 11 as in [15].
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For indexing of a reference sequence, the compressed genome contains the major alleles.
For indexing of a reference space, GSNAP also accesses a second compressed genome that contains the minor alleles.
downloaded all complete genome sequences of Bacteria, Virus from NCBI ftp site ftp://ftp.ncbi.nih.gov/genomes/; removed the plasmid sequence and any other non-human-related sequence; kept only one best genome sequence representing every species based on the assembly result; built the alignment index of reference sequence for classing sequence reads.
It provides dual functionality by aiding in alignment and stabilization of the fibular segments and concomitantly providing patient-specific anatomic references for indexing of bony and soft tissue components.
Such works, however, need an index for ease of reference, and it is unlikely that alphabetical order will be superseded except in specialized works.
Figure 1 describes the underlying data structure and the method for constructing a hybrid index of a reference sequence.
For example, SSAHA2, AGILE and SeqAlto use a hash table (HT) index of a reference genome, whereas BWA, SOAP2 and Bowtie2 use an index of the reference genome based on the Burrows–Wheeler transform [ 10].
This is typically performed by passing it through an index of the reference genome [8] [14], or by indexing the reads and searching the reference genome [15], [16].
BWT methods create a Burrows-Wheeler index of the reference sequence and efficiently search for perfect matches.
Statistical error matrices together with nonparametric Kappa index were used for comparison of reference data and classification result (Robertson and King 2011; Dabboor et al. 2014).
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