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technical.plos.txt
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technical/biomed/1471-2091-3-4.txt: AES, atomic emission spectroscopy; bp, base pairs; CD,
technical/biomed/1471-2105-2-8.txt: ) for all base paired positions
technical/biomed/1471-2105-2-8.txt: base pairs. This involves making an independence
technical/biomed/1471-2105-2-8.txt: the aligned base pairs as the average of these two
technical/biomed/1471-2105-2-8.txt: the various sorts of base pairs (GC, AU, GU) in a single
technical/biomed/1471-2105-2-9.txt: bases are not equal, a one base pair gap is inserted
technical/biomed/1471-2105-3-18.txt: using an objective function that includes base pairing
technical/biomed/1471-2105-3-18.txt: interactions, primarily Watson-Crick base pairs but also
technical/biomed/1471-2105-3-18.txt: permitting noncanonical base pairs. This RNA structural
technical/biomed/1471-2105-3-18.txt: that are associated with base pairs and single-stranded
technical/biomed/1471-2105-3-18.txt: that it can transition to. Consensus base pairs will be
technical/biomed/1471-2105-3-18.txt: consensus base pair; but it will also contain several
technical/biomed/1471-2105-3-18.txt: Given the consensus structure, consensus base pairs
technical/biomed/1471-2105-3-18.txt: structure. For example, for a consensus base pair,
technical/biomed/1471-2105-3-18.txt: about 55-60% are involved in consensus base pairs. The
technical/biomed/1471-2105-3-2.txt: the occurrence of G:C, A:U, or G:U base pairs that occur
technical/biomed/1471-2105-3-2.txt: etc. ) and base pairs that form
technical/biomed/1471-2105-3-2.txt: 97-98% of the secondary and tertiary structure base pairs
technical/biomed/1471-2105-3-2.txt: earlier), searches for helices and base pairs that are
technical/biomed/1471-2105-3-2.txt: maintaining G:C, A:U, and G:U base pairs. As more
technical/biomed/1471-2105-3-2.txt: eliminating previously proposed base pairs that are not
technical/biomed/1471-2105-3-2.txt: new secondary and tertiary structure base pairs that do
technical/biomed/1471-2105-3-2.txt: secondary structure base pairs and a few of the
technical/biomed/1471-2105-3-2.txt: tertiary structure base pairs predicted with
technical/biomed/1471-2105-3-2.txt: 23S rRNA base pairs predicted with covariation analysis
technical/biomed/1471-2105-3-2.txt: CRW Site. However, while nearly all of the base pairs
technical/biomed/1471-2105-3-2.txt: predict many of the tertiary base pairings in the
technical/biomed/1471-2105-3-2.txt: of the secondary structure base pairings.
technical/biomed/1471-2105-3-2.txt: Beyond the base pairs predicted with covariation
technical/biomed/1471-2105-3-2.txt: each base pair, as predicted by covariation analysis.
technical/biomed/1471-2105-3-2.txt: base pairs, small closed circles for G:U, large open
technical/biomed/1471-2105-3-2.txt: base pair) have the greatest amount of covariation;
technical/biomed/1471-2105-3-2.txt: base pairs. Base pairs with a green, black, grey, or
technical/biomed/1471-2105-3-2.txt: and 2C. Note that the majority of the base pairs in the
technical/biomed/1471-2105-3-2.txt: 16S and 23S rRNA have a red base pair symbol, our
technical/biomed/1471-2105-3-2.txt: some base pairs in the 16S and 23S rRNAs that have a
technical/biomed/1471-2105-3-2.txt: the global arrangement of the base pairs. For the
technical/biomed/1471-2105-3-2.txt: the secondary structure base pairs shown in blue above
technical/biomed/1471-2105-3-2.txt: base pairs and base triples are shown in red and green,
technical/biomed/1471-2105-3-2.txt: higher-order organization of the base pairs predicted
technical/biomed/1471-2105-3-2.txt: two alternative formats. The majority of the base pairs
technical/biomed/1471-2105-3-2.txt: base pair in each version of the 16S and 23S rRNA
technical/biomed/1471-2105-3-2.txt: and 23S [ 19 ] rRNA models. Every base pair in each of
technical/biomed/1471-2105-3-2.txt: base pairs were taken out of the structure model when
technical/biomed/1471-2105-3-2.txt: a G:C, A:U, or G:U base pair was greater than our
technical/biomed/1471-2105-3-2.txt: for those base pairs are available from the "Lousy
technical/biomed/1471-2105-3-2.txt: section. New base pairs were proposed when a (new)
technical/biomed/1471-2105-3-2.txt: 579 proposed 16S rRNA base pairs evaluated against six
technical/biomed/1471-2105-3-2.txt: compare the numbers of sequences and base pairs
technical/biomed/1471-2105-3-2.txt: sequences and base pairs in the current structure model
technical/biomed/1471-2105-3-2.txt: (478 base pairs and approximately 7000 sequences for
technical/biomed/1471-2105-3-2.txt: 16S rRNA, and 870 base pairs and approximately 1050
technical/biomed/1471-2105-3-2.txt: rRNA); and 3) all previously proposed base pairs that
technical/biomed/1471-2105-3-2.txt: rRNA base pairs predicted in the initial structure
technical/biomed/1471-2105-3-2.txt: either base paired or unpaired. Base paired nucleotides
technical/biomed/1471-2105-3-2.txt: heterogeneous collection of base pair interactions.
technical/biomed/1471-2105-3-2.txt: These include any non-canonical base pair (not a G:C,
technical/biomed/1471-2105-3-2.txt: pairs (when both positions in a base pair are not
technical/biomed/1471-2105-3-2.txt: flanked by two nucleotides that are base paired to one
technical/biomed/1471-2105-3-2.txt: another), base pairs in a pseudoknot arrangement, and
technical/biomed/1471-2105-3-2.txt: base pair). Each of these base pair categories has a
technical/biomed/1471-2105-3-2.txt: are base paired, nucleotides can also be unpaired in
technical/biomed/1471-2105-3-2.txt: for single positions, base pairs, and base triples for
technical/biomed/1471-2105-3-2.txt: all base pairs in the current covariation-based
technical/biomed/1471-2105-3-2.txt: structure models, b) tentative base pairs predicted
technical/biomed/1471-2105-3-2.txt: with covariation analysis, and c) base pairs previously
technical/biomed/1471-2105-3-2.txt: "Lousy" base pairs). Base triples are interactions
technical/biomed/1471-2105-3-2.txt: between a base pair and a third unpaired nucleotide;
technical/biomed/1471-2105-3-2.txt: the three types of tables: single bases, base pairs,
technical/biomed/1471-2105-3-2.txt: and base triples. Clicking on a position, base pair, or
technical/biomed/1471-2105-3-2.txt: (H-2A.2) used to predict the base pair is obtained,
technical/biomed/1471-2105-3-2.txt: link on the right-hand side of the base pair frequency
technical/biomed/1471-2105-3-2.txt: confidence rating for the base pairs predicted with the
technical/biomed/1471-2105-3-2.txt: extent of base pair types and their mutual exchange
technical/biomed/1471-2105-3-2.txt: predicted base pair. Red, our highest confidence
technical/biomed/1471-2105-3-2.txt: rating, denotes base pairs with the highest scores and
technical/biomed/1471-2105-3-2.txt: contains at least one red base pair. Base pairs with a
technical/biomed/1471-2105-3-2.txt: red base pair. Black base pairs have a lower
technical/biomed/1471-2105-3-2.txt: covariation score, while grey base pairs are invariant,
technical/biomed/1471-2105-3-2.txt: base pairs do not satisfy these constraints;
technical/biomed/1471-2105-3-2.txt: The covariation score for each base pair is
technical/biomed/1471-2105-3-2.txt: each base pair is equivalent to the highest ranking
technical/biomed/1471-2105-3-2.txt: 927:1390 base pair in 16S rRNA (Figure 2C; H-2A). Note
technical/biomed/1471-2105-3-2.txt: that the entry for the 927:1390 base pair (H-2A) in the
technical/biomed/1471-2105-3-2.txt: list of base pairs in the left frame is red in the C
technical/biomed/1471-2105-3-2.txt: (or confidence) column. For this base pair, only the T
technical/biomed/1471-2105-3-2.txt: a G:U base pair, A:U base pair at 16.2%, U:A at 6.9%,
technical/biomed/1471-2105-3-2.txt: or G:G base pair (H-2A.1). The collective scoring data
technical/biomed/1471-2105-3-2.txt: 928:1389 and 929:1388 base pairs are also both red.
technical/biomed/1471-2105-3-2.txt: extents of covariation for both base pairs and are thus
technical/biomed/1471-2105-3-2.txt: changes displayed for the base pairs and base triples.
technical/biomed/1471-2105-3-2.txt: for the three types of data, single bases, base pairs,
technical/biomed/1471-2105-3-2.txt: and base triples. Clicking on a position, base pair, or
technical/biomed/1471-2105-3-2.txt: base, base pair, or base triple. The presentation for
technical/biomed/1471-2105-3-2.txt: single bases, this number is in black. For base pairs,
technical/biomed/1471-2105-3-2.txt: The base pair types that result from a mutual change
technical/biomed/1471-2105-3-2.txt: adjacent nucleotides, base pairs, three nucleotides,
technical/biomed/1471-2105-3-2.txt: 2) nucleotide and base pair frequency tables for all
technical/biomed/1471-2105-3-2.txt: and base pair frequency tables for more phylogenetic groups
technical/biomed/1471-2105-3-2.txt: nucleotide and base pair frequency tables when the
technical/biomed/1471-2105-3-24.txt: approximately every thousand base pairs [ 7 8 9 ] . Given
technical/biomed/1471-2105-4-27.txt: to, and interrogates the expression of a 25 base pair
technical/biomed/1471-2121-1-2.txt: aa, amino acid; Ab, antibody; bp, base pair; CaPO
technical/biomed/1471-2121-3-10.txt: both encode a 10-base pair sequence that is identical to
technical/biomed/1471-2121-3-10.txt: the P3 sequence with an insertion of 3 base pairs at
technical/biomed/1471-213X-1-4.txt: the bpA. These two enzymes are rare eight base pair
technical/biomed/1471-2156-2-17.txt: The DMD gene spans 2.4 million base pairs of genomic DNA
technical/biomed/1471-2156-2-17.txt: gene (2.4 million base pairs), finding 100% of mutations is
technical/biomed/1471-2156-2-3.txt: three exons. The first exon contains 279 base pairs (bp)
technical/biomed/1471-2156-2-7.txt: Then, 5 μl of the PCR product (375 base pairs) was
technical/biomed/1471-2156-2-7.txt: products, 200 and 175 base pairs (A allele). The G to A
technical/biomed/1471-2156-3-16.txt: chromosomes have as few as 3-5 base pairs between the
technical/biomed/1471-2156-3-4.txt: TRP1 flanked by 200-base pair (bp)
technical/biomed/1471-2164-2-1.txt: date, extending over more than 1 megabase pairs of genomic
technical/biomed/1471-2164-2-4.txt: because of the correct base pair formed at the 3' end and
technical/biomed/1471-2164-2-4.txt: correctly base paired ends.
technical/biomed/1471-2164-2-4.txt: this assay to genotype any SNP regardless of the base pair
technical/biomed/1471-2164-2-7.txt: addition to the 93 base pairs from the E0 sequence and the
technical/biomed/1471-2164-3-13.txt: and the base pairing of the branch point with the U2RNA
technical/biomed/1471-2164-3-13.txt: the U1snRNP is mainly directed by RNA-RNA base pairing [
technical/biomed/1471-2164-3-31.txt: generated by RNase H; and 2) adding a few base pairs to
technical/biomed/1471-2164-3-35.txt: contains an A-rich stretch of 30 base pairs with 23 A
technical/biomed/1471-2164-3-35.txt: base pairs give the strongest hybridization signals.
technical/biomed/1471-2164-3-35.txt: and has a somewhat longer insert length (622 base pairs).
technical/biomed/1471-2164-3-35.txt: not only in terms of Watson-Crick base pairing, but also in
technical/biomed/1471-2164-3-6.txt: are two leucine zippers starting at base pairs 484 and
technical/biomed/1471-2164-3-7.txt: the detection window of 45 to 900 base pairs and
technical/biomed/1471-2164-3-7.txt: increasing numbers of base pairs: NewHeight =
technical/biomed/1471-2164-3-7.txt: correspond to sequence length in base pairs better than
technical/biomed/1471-2164-3-7.txt: analysis, MA - mixed analysis, bp - base pairs, StDev -
technical/biomed/1471-2164-4-14.txt: BGH037 amplify an ~180 base pair (bp) fragment from the
technical/biomed/1471-2164-4-16.txt: tolerant to insertion of up to 125 base pairs between the
technical/biomed/1471-2164-4-2.txt: base pair region spanning the polyadenylation signal in
technical/biomed/1471-2164-4-21.txt: the base pairing between the probe and target, but
technical/biomed/1471-2164-4-21.txt: the probes was conserved but the base pairing in the
technical/biomed/1471-2164-4-21.txt: the base paired region resulted in greatly decreased
technical/biomed/1471-2164-4-25.txt: million base pairs of genomic sequence surrounding the peak
technical/biomed/1471-2164-4-25.txt: Figure 1with base pair 1 starting at the 5-prime end of
technical/biomed/1471-2164-4-25.txt: The two million base pairs of index genomic sequence
technical/biomed/1471-2164-4-25.txt: amplicon was designed to be between 90 and 150 base pairs
technical/biomed/1471-2180-1-12.txt: within ∼ 18 base pairs of the 3' end of the growing DNA
technical/biomed/1471-2180-1-31.txt: then made against this ORF and the 1578 base pair gene
technical/biomed/1471-2180-1-34.txt: anti-P dsRNA in which the lowercase A-U base pair (see
technical/biomed/1471-2180-1-34.txt: lowercase a-u base pair was changed to g-c (see
technical/biomed/1471-2180-2-13.txt: ) by one base pair (bp) in the right half-site (e.g., A
technical/biomed/1471-2180-2-38.txt: few nucleotides over a 2,400 base pair coding sequence.
technical/biomed/1471-2180-3-13.txt: variation in the type of RNA/RNA base pairing occurs
technical/biomed/1471-2180-3-13.txt: maintain base pairs in stems. Thus the large divergence
technical/biomed/1471-2180-3-13.txt: intra- and inter- molecular base pairings, i.e., stem
technical/biomed/1471-2180-3-13.txt: loop a and stem 2 (Figure 12). Compensatory base pair
technical/biomed/1471-2180-3-13.txt: nt, nucleotides; bp, base pairs
technical/biomed/1471-2180-3-15.txt: reaction; bp - base pair; kb - kilobase; ATCC - American
technical/biomed/1471-2199-2-12.txt: 200, 250, and 500 base pairs, with the 500 base pair band
technical/biomed/1471-2199-2-12.txt: major band of approximately 480 base pairs was observed
technical/biomed/1471-2199-2-12.txt: 480 and 400 base pairs were observed (Fig. 2A). Nested
technical/biomed/1471-2199-2-12.txt: RLM-RACE, a faint band of approximately 150 base pairs
technical/biomed/1471-2199-2-12.txt: containing ~500 base pairs upstream of the ATG start codon
technical/biomed/1471-2199-2-12.txt: 435 base pairs upstream of the ATG was inactive [ 35 ] .
technical/biomed/1471-2199-2-12.txt: positioned ~30 base pairs downstream of an AT-rich element
technical/biomed/1471-2199-2-5.txt: indicate the mutated base pairs.
technical/biomed/1471-2199-3-17.txt: purine and/or base pair at that position, whereas G3C and
technical/biomed/1471-2199-3-17.txt: restored base pairing were also identified. Further, the
technical/biomed/1471-2199-3-17.txt: show selection for a Watson-Crick base pair at the
technical/biomed/1471-2199-3-17.txt: the downstream base pair whenever there was an upstream
technical/biomed/1471-2202-2-12.txt: found to have the expected size of 420 base pairs.
technical/biomed/1471-2202-3-16.txt: out using forty-eight base pair oligonucleotide probes,
technical/biomed/1471-2202-3-7.txt: sequence flanked by the inverted 19 base pair repeats known
technical/biomed/1471-2202-3-7.txt: complex process that involves generating a 9 base pair
technical/biomed/1471-2202-3-7.txt: subsequently repaired to produce a 9 base pair duplication
technical/biomed/1471-2210-2-14.txt: base pairs in the 3'UTR compared with REP2-2.7. It is
technical/biomed/1471-2210-2-14.txt: created an open reading frame of 1,083 base pairs with an
technical/biomed/1471-2229-2-3.txt: stringency with a 300 base pair homologous
technical/biomed/1471-2229-2-3.txt: conducted at high stringency with a 1700 base pair
technical/biomed/1471-2229-2-3.txt: approximately 100 base pairs for ease of visualization on
technical/biomed/1471-2229-2-3.txt: amplification product of 579 base pairs. Primer pair T-21
technical/biomed/1471-2229-2-3.txt: 455 base pairs. Primers T-31 and T-32 correspond to
technical/biomed/1471-2229-2-3.txt: transcript-3 and amplify a 362 base pair product. Lastly,
technical/biomed/1471-2229-2-3.txt: produce a 238 base pair amplification product. The
technical/biomed/1471-2229-2-3.txt: was a 300 base pair digoxigenin labeled PCR product.
technical/biomed/1471-2229-2-3.txt: analysis was a 1700 base pair PCR product.
technical/biomed/1471-2229-2-3.txt: A 300 base pair cDNA probe corresponding to nucleotide
technical/biomed/1471-2229-2-3.txt: blot analysis. An approximately 1700 base pair cDNA probe
technical/biomed/1471-2334-3-12.txt: introduction of mismatched base pairs. The effectiveness of
technical/biomed/1471-2350-2-2.txt: Then, 5 μl of the PCR product (265 base pairs) was
technical/biomed/1471-2350-2-2.txt: yielded two products, 69 and 196 base pairs (f allele),
technical/biomed/1471-2350-2-8.txt: Lithuania) digestion of a 244-base pair PCR-amplified
technical/biomed/1471-2377-3-4.txt: of a variable number of tandem repeats of 39 base pairs,
technical/biomed/1471-2458-3-5.txt: OL26 and JWA-1b generates an amplicon of ~292 base pairs
technical/biomed/1471-2474-2-1.txt: a 287 base pair fragment of intron 16 [ 13]. Patients may
technical/biomed/1471-2474-2-1.txt: fragments (86, 46, and 37 base pairs) in the normal
technical/biomed/1471-2474-2-1.txt: allele and two fragments (123 and 46 base pairs) in the
technical/biomed/1472-6750-1-13.txt: incorporation of single base pair substitutions in the
technical/biomed/1472-6750-1-13.txt: 748 were screened along with all possible single base pair
technical/biomed/1475-4924-1-5.txt: sequence located within a few hundred base pairs of the
technical/biomed/1475-4924-1-5.txt: base pairs away from the promoter. These regulatory modules
technical/biomed/1475-4924-1-5.txt: nearly 125 kilo-base pairs (kbp) in length, with a
technical/biomed/1477-7827-1-23.txt: base pair region of OSU-T1-50 had significant homology
technical/biomed/ar297.txt: PCR products of the expected 350 base pair (bp) length
technical/biomed/ar409.txt: fragment (~800 base pairs) was prepared by PCR and
technical/biomed/ar774.txt: single base pair within the highly conserved reverse
technical/biomed/ar774.txt: bp = base pair(s); EMSA = electrophoretic mobility shift
technical/biomed/bcr570.txt: bp = base pairs; PCR = polymerase chain reaction.
technical/biomed/bcr571.txt: bp = base pairs; FISH = fluorescence
technical/biomed/bcr602.txt: of 225 base pairs. The internal control for all samples
technical/biomed/bcr631.txt: size by 30 base pairs. These two products were cloned
technical/biomed/gb-2000-1-1-research002.txt: of intronic sequence - 15,337 base pairs (bp) from
technical/biomed/gb-2001-2-12-research0054.txt: three base pairs:TTG--- for the -35 region and TA---T for
technical/biomed/gb-2001-2-3-research0008.txt: between 400 and 800 base pairs (511 base pairs ± 197 base
technical/biomed/gb-2001-2-3-research0008.txt: library range between 139 to 1,746 base pairs (bp),
technical/biomed/gb-2001-2-4-research0010.txt: necessarily true because of Watson-Crick base pairing.
technical/biomed/gb-2001-2-4-research0011.txt: sequenced to completion, yielding a 1,036 base pair (bp)
technical/biomed/gb-2001-2-4-research0014.txt: range of 200-1,000 base pairs (bp) are optimal.
technical/biomed/gb-2001-2-6-research0021.txt: a span of 69,034 base pairs [ 2]. Human mitochondrial DNA
technical/biomed/gb-2001-2-6-research0021.txt: 2 rRNAs and 22 tRNAs) over 16,569 base pairs [ 3]. All
technical/biomed/gb-2001-2-7-research0025.txt: the 3.2 billion base pair (bp) human genome is
technical/biomed/gb-2001-2-7-research0025.txt: obtain a median of 0.017 entries per base pair for known
technical/biomed/gb-2001-2-7-research0025.txt: genes and 0.005 entries per base pair for anonymous
technical/biomed/gb-2001-2-8-research0027.txt: seven different microbial genomes, using 25 base pairs
technical/biomed/gb-2002-3-10-research0053.txt: content of 430 million base pairs (Mbp), the rice genome is
technical/biomed/gb-2002-3-10-research0053.txt: base pairs (2.5 Gbp) and that of wheat (
technical/biomed/gb-2002-3-12-research0079.txt: 98.7% of the base pairs are contained within 100-kb
technical/biomed/gb-2002-3-12-research0079.txt: and the total number of base pairs involved in those
technical/biomed/gb-2002-3-12-research0083.txt: hundred base pairs, and the separation can be as much
technical/biomed/gb-2002-3-6-research0029.txt: micro-exons, ranging from 3 to 25 base pairs (bp) in
technical/biomed/gb-2003-4-4-r24.txt: important considering that within a few hundred base pairs,
technical/biomed/rr196.txt: approximately 500 base pairs upstream of the stop codon,