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The number of experiments on the same factor and same lever is L in total, and the virtual sequence number is q, q = 1 ~ L.
Total variance method transforms time-offset data to frequency-offset data and extends the data to be a virtual sequence nearly as three times long as the initial data by mapping.
Public databases such as DNA Data Bank of Japan do not accept virtual sequence for the registration.
The PSSM chaining problem for a single sequence S j can be considered a chaining problem for pairwise matches between sequence S j and a virtual sequence V[1.. L] such that a match for PSSM M i is a match of length one at position i in V.
If a reference sequence covering the PCR region was not available, we constructed a new virtual sequence by de novo assembly using the Sequencher Ver. 5.0.1 DNA sequence assembly software (Gene Code, Ann Arbor, MI), and used it as a reference sequence.
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A query using the tag sequence as the primary key allowed us to match experimental sequences (CplusTag), virtual sequences (Preditag) and selected annotations, thus generating a table of results.
Public databases do not accept virtual sequences.
Virtual sequences were mapped to the PAR-masked genome and mappable reads were extracted.
The retrotransposon sequences reconstructed in our analyses are actually "virtual" sequences that could not correspond to specific loci, impeding their use for dating.
We identified obvious candidate virtual spots for 60/96 spots mapped in the BXD data (Fig 6A) and 140/167 spots mapped with the BSS data (Fig 6B) for a total of 200 C57BL/6 spot candidate virtual sequences.
The purpose of the module was to (1) demonstrate how virtual sequences can be assayed for biological function and (2) determine whether the TPase encoded by Ping is sufficient for excision or whether ORF1 is also required.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com