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Table 2 Nucleotide Position 1 Position 2 Position 3
"... In PAGE 29: ...ite is predicted at position 405 with a confidence of 0.94. The mutated version of the CDS does not result in any splice site predictions. Table2 : The nucleotide distribution at the three codon positions for the translated exon sequence in A. thaliana.... ..."
TABLE I The molecular neuron strings with their nucleotide sequences
Table 1: IUPAC Alphabet for Nucleotide Sequences
2003
"... In PAGE 3: ... In our approach, motifs are represented by IUPAC patterns or patterns with degenerate symbols. The IUPAC alphabet is shown in Table1 . When searching for the best motifs, we evaluate every possible pattern using both methods.... In PAGE 6: ... The pattern trie coresponds to the space of IUPAC patterns. The pattern trie is a rooted trie of maximum depth l with each branch labeled with one of the IUPAC symbols in Table1 . Each leaf node (of depth l) corresponds to the IUPAC pattern of length l defined by the path from the root of the pattern trie to the leaf.... ..."
TABLE 1 Sequences of Primer and Probe Nucleotides
Table 1 shows the genetic code. Table 2 shows the IUPAC ambiguity codes. Table 1 is reinterpreted in Table 3, which contains the nucleotide sequences (using the IUPAC ambiguity codes) for each of the 20 amino acids along with their degeneracy.
"... In PAGE 2: ... Clustering techniques require a concept of similarity and/or distance between members. The second Table1 . Genetic code table T C A G T TTT Phe (F) TTC TTA Leu (L) TTG TCT Ser (S) TCC TCA TCG TAT Tyr (Y) TAC TAA Ter TAG Ter TGT Cys (C) TGC TGA Ter TGG Trp (W) C CTT Leu (L) CTC CTA CTG CCT Pro (P) CCC CCA CCG CAT His (H) CAC CAA Gln (Q) CAG CGT Arg (R) CGC CGA CGG A ATT Ile (I) ATC ATA ATG Met (M) ACT Thr (T) ACC ACA ACG AAT Asn (N) AAC AAA Lys (K) AAG AGT Ser (S) AGC AGA Arg (R) AGG G GTT Val (V) GTC GTA GTG GCT Ala (A) GCC GCA GCG GAT Asp (D) GAC GAA Glu (E) GAG GGT Gly (G) GGC GGA GGG ... In PAGE 3: ... The BlockSimilarity score uses a similarity metric between amino acids, which is based on their coding in the Genetic Code. As explained later in detail, two amino acids are considered similar if they are identical, or if they are in the same row or column of the Genetic Code Table (see Table1 ). Once conserved amino acid blocks are found, degenerate primers are designed by reverse translating the conserved blocks to nucleotide sequences using the genetic code.... In PAGE 3: ... It suggests, for example, that for the purpose of designing degenerate primers, Cysteine (C) and Tyrosine (Y) ought to be considered as similar , since they can be represented by the nucleotide sequences TGY and TAY, respectively, which differ only in the middle base. The similarity of Cysteine and Tyrosine, in this sense, is a consequence of their position in the genetic code table ( Table1 ), i.... ..."
Table 3: Nucleotide Compositions and CG Content of Human Genome*
2003
"... In PAGE 3: ...able 2: Current Status of Human Genome Sequencing Process (Jan 5, 2003)*.......17 Table3... ..."
(Table 3). In nucleotide-based analysis, the G models recovered T1 as the ML tree in 45 to 46 genes, whereas all other nucleotide models performed better and recov- ered T1 in 52 to 56 genes, similar to codon-based analysis, in which the number is 51 to 54. The poor performance of the amino acid models is due to loss of phylogenetic information when the DNA sequences are translated into proteins. This interpretation receives more support when we consider the numbers of genes that support individual clades (defined by nodes 1 to 5) in tree T1 of Figure 1, shown in Table 3. Clade 4 is defined by a long branch and is recovered in almost all analyses and mod-
"... In PAGE 10: ... Deep nodes 4 and 5 (Fig. 1a) might be expected tobeaffectedbynonhomogenousbasecompositions,but they were recovered in most genes by the codon or nu- cleotide C models (Table3 ). The poorer performance in recovering recent nodes 2 and 3 (Table 3) appeared to be due to the short internal branch lengths or lack of phylogenetic resolution, as base compositions among the recent species are quite homogeneous.... In PAGE 10: ...odated. Deep nodes 4 and 5 (Fig. 1a) might be expected tobeaffectedbynonhomogenousbasecompositions,but they were recovered in most genes by the codon or nu- cleotide C models (Table 3). The poorer performance in recovering recent nodes 2 and 3 (Table3 ) appeared to be due to the short internal branch lengths or lack of phylogenetic resolution, as base compositions among the recent species are quite homogeneous. Instead, loss of information in the amino acid sequences appears to be a more serious concern for those data.... ..."
Table 1 The 20 amino acids and their corresponding nucleotide sequences
"... In PAGE 2: ... The primary structure is the sequence of amino acids obtained from the nucleotide sequence. Table1 lists the 20 animo acids Table 1 The 20 amino acids and their corresponding nucleotide sequences... ..."
Table 1: Compression of DNA Sequences (bits/nucleotide)
1998
"... In PAGE 6: ... Yeast chromosome III was included as a long string, 315K nucleotides. Table1 gives the coding figures for biocompress2 (Grum- bach and Taji 1994) and CDNA-compress (Loewenstern and Yianilos 1997), the first two columns coming from the lat- ter paper, compared with the new string model. The figures for HUMHBB, CHNTXX and Yeast chrIII are from the ap- proximate algorithm set to run in realistic times and are thus upper-bounds on the true entropies under the model.... ..."
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