Noncoding sequence classification based on wavelet transform analysis: part II
Omar ParedesMarija StrojnikMichelle K. SchollJ. Alejandro MoralesRebeca Romo‐VázquezHugo Vélez‐PérezRadu RantaGuillermo García–Torales
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Abstract:
DNA sequences in human genome can be divided into the coding and noncoding ones. We hypothesize that the characteristic periodicities of the noncoding sequences are related to their function. We describe the procedure to identify these characteristic periodicities using the wavelet analysis. Our results show that three groups of noncoding sequences, each one with different biological function, may be differentiated by their wavelet coefficients within specific frequency range.Keywords:
Coding region
Complementary sequences
A general method for construction of polyphase complementary pairs of sequences of length 2N is presented. This method is based on the recursive algorithms introduced by Golay for binary sequences and by Sivaswamy for polyphase sequences. A modification of the proposed algorithm can generate multilevel and complex sequences of magnitude different from unity. The proposed sequences are suitable for radar applications where complementary sequences different from the known binary sequences are required.
Polyphase system
Complementary sequences
Binary Golay code
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Sequences with perfect correlation properties (i.e., vanishing sidelobes of their autocorrelation function) are applied in navigational systems, in synchronization, and for system measurement and identification. Since only one periodic perfect binary sequence (length N=4) is known, on the one hand polyphase sequences with a larger phase alphabet, especially quadriphase sequences, and on the other hand so-called complementary sets of sequences have been applied (Golay 1961). Pairs of sequences are called aperiodic or periodic complementary sets (ACS or PCS) if the sum of their aperiodic or periodic respectively autocorrelation functions is a delta function. Complementary pairs of binary sequences cannot exist for all lengths. Therefore, sets of ternary sequences with the elements -1, 0 and 1 have been investigated. Since for technical reasons the number of zero-elements should be as small as possible, ternary complementary sets are called optimum if no set with a smaller number of zero-elements exists. Ternary aperiodic complementary sets have been investigated in Garvish and Lempel (1994). In this paper, the construction of new optimum PCS and almost perfect quadriphase sequences is described.
Complementary sequences
Aperiodic graph
Binary Golay code
Polyphase system
Sequence (biology)
Pseudorandom binary sequence
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To investigate the structure and sequence of SCF gene in goat, primers were designed based on the sequence of goat and sheep. Two transcript splices were obtained with PCR and cloning and bioinformatics analysis of the sequence was made. The results showed that the length of coding sequence of soluble and transmembrane SCF gene in goat is 825 bp and 741 bp, respectively. The length difference was due to the deletion / insertion of 6th exon. The identity of SCF gene between goat and sheep or cattle was 98% and 97%, respectively. The phylogenetic clusters based on SCF gene sequence of thirteen species were the same as the zootaxy.
Cloning (programming)
Coding region
Sequence (biology)
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Sequence (biology)
Complete sequence
Alignment-free sequence analysis
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With reference to the human interleukin 18 gene in GeneBank database, a pair of DNA primers was designed and synthesized. A 481bp fragment containing hIL-18 gene was successfully amplified by using RT-PCR and then cloned into PGEM-T plasmid, enzyme digested by EcoR I and Sal I indicated that there is one nucleotide different from the published hIL-18 cDNA sequence. The sequence analysis indicated that in the sequence of IL-18- PGEM-T contains all the coding sequence for mature protein of hIL-18. The result would promote the further research in molecular biology of hIL-18, such as the expression and the biological function research.
Coding region
Cloning (programming)
Sequence (biology)
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Objective To obtain the Eg10 gene of echinococcus granulosus and analyze its sequence.Methods Total RNA was extractedfrom protoscoleces of Echinococcus granulosus of humam origin.The specific primers were designed according to published nucleotide sequence in Genebank.The Eg10 gene fragment was amplified By RT-PCR and then cloned it into pGEM-T vector for sequencing and analyzing.Results The Eg10 sequence was successfully amplified,which was 938bp.The sequence and its amino acid sequence showed 100% homology with that published in Genebank previously.The deduced sequence of coding amino acid was 100% homology,too. Conclusion The sequenced Eg10 gene has a completely open coding frame(765bp).It will be significant to study its structure and function,as well as immunizing prevention.
Coding region
Homology
Cloning (programming)
Sequence (biology)
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Objective To amplify the 3'end gene sequence of voltage-dependent sodium channel from Aedes aegypti.Methods Total RNA was extracted from the female adult of Ae.aegypti,and a single stranded cDNA was reverse transcripted with Trsa,then to design the positive and negative control,a 3'end cDNA was amplified by nested PCR and 3'RACE technique,and cloning and sequence analysis were performed.Results A total of 809 bp PCR product was obtained,including the coding sequence with 208 amino acids and non-coding sequence with poly(A) tail.Similarity analysis by DNAstar 5.0 showed high similarity(about 65%) comparing to the same region of amino acid sequence from Musca domestica.Conclusion The 3'end cDNA sequence of voltage-dependent sodium channel from Ae.aegypti was successfully obtained.
Coding region
Cloning (programming)
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In this study,the coding sequence of porcine tumor suppressor candidate 5(TUSC5)were amplified based on the in silico sequence information. The result showed that the full length of TUSC5 was 636 bp and the open reading frame was 534 bp long. The predicted protein-coding sequence was 177 amino acid residues. Identity analysis showed that the nucleotide sequence of porcine TUSC5 shares 83.5%,82.4% and 82.6% with that of human,mouse and rat,respectively. The deduced protein sequence shares 71.2%,77.5%,and 78% homology with that of human,mouse and rat,respectively. All of these data indicates that the porcine TUSC5 gene was successfully cloned in the present study.
Coding region
Cloning (programming)
Homology
Sequence (biology)
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Golay complementary sequences play quite an important role in communication and radar. In this paper, we present a family of quaternary Golay complementary sequences. The resultant sequences result from conversion of the existing binary Golay sequences, and both have the same length and number of subsequences. Our method can provide rich quaternary Golay complementary sequences due to a large number of binary Golay complementary sequences available.
Binary Golay code
Complementary sequences
Ternary Golay code
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We cloned the LOC339524 gene in Sprague-Dawley (SD) rats and analyzed the structure and function of the protein encoded by it. Based on the known human LOC339524 gene sequences, the full-length coding sequence of the LOC339524 gene in SD rats was cloned and amplified by the polymerase chain reaction using the complementary DNA of SD rats as a template. Bioinformatics analysis showed that the length of the cloned LOC339524 gene (GenBank accession No. KM224520) was 831 bp and it encoded a deduced protein of 276 amino acids. Sequence analysis revealed that the coded protein was identical to that produced in humans and its functional domain was located in the 138-236 amino acid fragments, a proline-rich region. Our results suggest that the encoded protein may be a significant regulator of the inflammatory response and may provide sufficient information to justify an in-depth investigation of the role of the LOC339524 gene.
Cloning (programming)
Coding region
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