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VCF files generated by GAP were then uploaded into Ingenuity Variant Analysis tool (QIAGEN) for further variant filtering.
The majority of constructs used in this study were generated by gap repair in yeast (Uetz et al., 2000).
pFvL909 was generated by gap repair of pFvL230 using double-strand oligonucleotides to introduce an SV40 nuclear-localization signal (NLS) (PKKKRKV) [ 87] and a unique NruI site.
Plasmids pFvL914 and pFvL916 were generated by gap repair by co-transformation of the LexA-V5-Dot1 fromment from pFvL230 and pFvL908 digested with BsrGI-XbaI and pRS315 digested with AlwNI and EcoRI.
Linearized targeting constructs, generated by gap repair cloning containing mouse lincRNA upstream and downstream homology arms flanking a KOZAK-ATG lacZ-pA- LoxP-hUb1-EM7 neo(superscript R -pA- LoxP cassette, weR -pAectroporated into VGF1 hybrid mouse embryonic stem (ES) cells, derived from a 129S6S v/Ev female to a C57BL/6N male mating.
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To account for homoplasy generated by gaps, the gap creating regions were ignored (accounting for ~97 characters of aligned matrix).
These complexities must be interpreted in the context of the fact that recordings were obtained from single astrocytes in a network generated by their gap junction connections.
Codon aligned orthologous sequence pairs were generated by removing gaps, ambiguous regions including runs of single amino acids with gaps, misidentified introns or likely sequencing errors within poorly represented ESTs.
The method presented in this paper uses this set of damage indices from each mode generated by the Gapped-Smoothing Method (GSM), and suppresses the noise by allowing only those peaks which show the location of the damage.
And then paired-end reads were mapped to contigs to find out contigs derived from the same transcripts and the distance of them, the scaffolds were generated by filling gaps with N between these contigs.
Of those, 1662 clones (average insert size 2 kb) were picked from the HapMap chromosome 6 library [ 27] and 85 clones were generated by cloning gap-spanning PCR amplicons (average insert size 332 bp).
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