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Here, a DENV physicochemical property (PCP -consensus sequence was derived from 671 unique sequences from the Flavitrack database.
Unique sequences from the two NE strains were then aligned with each other to identify those conserved between them, and the ORFs present in these unique regions were retrieved.
The reason that Overgo hybridization strategy was successfully used in the construction of integrated genetic and physical maps was that Overgo probes were designed based on unique sequences from the genome sequences, not from repetitive sequences.
The unique sequence tags (UStags) method [13] was used to process the FT MS/MS data using the ICR2LS developed in-house (http://ncrr.pnl.gov/software/), and only unique sequences from the IPI human sequence database (ipi.HUMAN.v3.39 downloaded from ftp://ftp.ebi.ac.uk/pub/databases/IPI/) were used for identification of the peptidome peptides.
We identified 55,641 unique sequences from the dataset.
Only 864 unique sequences from the 454 dataset overlapped with other ESTs.
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In addition, unmodified oligonucleotide probes (80 mer) targeted to a unique sequence from the coding region of each gene were spotted on the same macroarray.
To accurately determine the levels of specific eIF4G variants, we generated isoform-specific, polyclonal antibodies using peptides corresponding to a unique sequence from the N-terminus of each isoform (see Materials and Methods).
The generated sequences were analyzed by the program Bioedit v.7.0.9 [ 14] to generate a unique sequence from the bidirectional sequence data.
Using in silico analysis coupled with PCR verification, we found no convincing evidence of breakpoints between the wAnaITG and D. ananassae nuclear unique sequence from the euchromatic chromosomes X, 2, and 3.
We also included a set of control regions, including CASP12 (13 kb) for which we had the Sanger capillary sequencing data from some of the same individuals (Xue et al. 2006) and 20 kb of unique sequence from the Y chromosome, where there should be no reads mapping in females and no heterozygote calls in males.
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