Sentence examples for map the repeats from inspiring English sources
Given the variable number of residues at the N-terminal end of these units, sequence databases tend to map the repeats of WD-proteins between GH and WD dipeptides for convenience.
The 'Repeats map' was developed using Perl, MISA and Blastn [ 39] programs for identifying similarities among the sequences and mapping the repeats.
This suggested that approximately one third of the B. tryoni genome consists of repetitive DNA (~31.4% of reads mapped to the repeats with mapping quality q > 20, NM = 4.9 where NM is the SAM flag indicating the number of mismatches).
Prior to mapping, the repeat regions in the reference genome were masked using RepeatMasker [ 30].
All human promoters not mapped in the first step (i.e. orthology mapping) were mapped to the repeat-masked target genome and only those promoters mapped uniquely to the target genome were reported.
SIDER annotations were combined to in-silico mRNA extremity predictions to generate a detailed distribution map of the repeat family, hence uncovering an enrichment of antisense-oriented SIDER repeats between the polyadenylation and trans-splicing sites of intergenic regions, in contrast to the exclusive sense orientation of SIDER elements within 3'UTRs.
Reads mapped on the repeated regions were discarded.
First, CAGE tags were mapped at the repeat-masked human genome, thus excluding so-called "GC-rich low-complexity regions" and simple repeats such as (CCCCG n.
The unmapped promoters were then re-mapped to the repeat-masked target genome using blastn with the following modified parameters: −penalty −3 -reward 1 -gapopen 3 -gapextend 3. Promoters were considered single mappers if they were uniquely mapped.
Our conclusion is that the optimal reference sequences for scoring RADseq markers for linkage mapping is the repeat masked draft genome, not the unmasked genome, and not the gene models.
Mouse promoters were derived from FANTOM5 CAGE data in the same way as that described for the human promoters and were mapped to the repeat-masked mouse genome (mm9) as downloaded from Ensembl (API 67).
