![]() Azenta Life Sciences Consumables & Instruments.Gene Synthesis & Cloning/Mutagenesis FAQs.CLIA Variant Confirmation (PCR + Sanger).This application of softmasking applied to problem of long read assembly is described on this blog. Soft masked (low complexity) regions are not used for matches of seeds, but they are used only for the extension of the alignment if there was a seed in a neighbouring region. Mapping of sequence to reference usually starts with perfect matches of seeds (substrings) of the mapped reads and the reference sequence. I would guess that the reliability of the softmasked regions of mouse genome will very high. However, this will be problem for non-model organisms. IMHO, low complexity regions are always more likely to be missassembled than high complexity sequences. Studied organisms do not have good repeat libraries available for The location and identity of repeats found by RepeatMasker are also Identified by WindowMasker, have been masked to lower-case. ![]() Repetitive sequences in eukaryotic genome assembly sequence files, as How exactly the genome was masked you can find in FAQ of NCBI:Īre repetitive sequences in eukaryotic genomes masked?
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