PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Base Sequence”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed2006

Sequence-based typing of the complete coding sequence of DQA1 and phenotype frequencies in the Dutch Caucasian population.

Typing of DQA1 by sequencing has been a challenge because of a 3-nucleotide deletion in exon 2 in half of the alleles. Furthermore, 19 of the 28 alleles cannot be identified on basis of exon 2 alone, but need additional exon information. With the sequencing strategy presented here the complete exons 1-4 are sequenced heterozygously, enabling identification of all DQA1 alleles by sequence-based typing (SBT). Exons 1-4 were amplified and sequenced separately, the combined sequences were used for automated allele assignment. The method was validated by typing 21 individuals with all possible different allele group combinations. In addition 26 quality control samples were correctly typed by this method. To determine the phenotype frequencies 155 unrelated Dutch Caucasian individuals were DQA1 typed. In total 15 known and two new DQA1 alleles were identified. DQA1*0103 and *0505 were the most frequent alleles with phenotype frequencies of 30% and 29%, respectively. The SBT method presented here is an improvement compared to already existing protocols in that the complete exon sequence is obtained for all coding exons, using identical polymerase chain reaction conditions. Furthermore, all exons are sequenced heterozygously, facilitating allele assignment and reducing the number of amplification reactions.

Alleles↗
PubMed2005

Comparative mapping of sequence-based and structure-based protein domains.

BACKGROUND: Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. METHODS: Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam) and the other structure-based (SCOP). A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. RESULTS: The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.

Algorithms↗
PubMed1993

Crystal packing effects on A-DNA helix parameters: a comparative study of the isoforms of the tetragonal & hexagonal family of octamers with differing base sequences.

The helix and base pair parameters of A-DNA octamers have been compared having different base sequences both in the tetragonal and hexagonal crystal systems. For the eight structures in the tetragonal family, the twist, rise, slide, inclination and tilt are essentially the same, influenced by the similarity in crystal packing. The propeller twist and the base pair buckle display small sequence dependent variations. But the base pair roll appears to be changed by the specific intermolecular hydrogen bonding interactions. For four of the five octamer structures in the hexagonal family, the base pair rise, slide, inclination, tilt, as well as the propeller twist and buckle are all very similar, while the twist angle and the base pair roll are not. The intermolecular hydrogen bonding interactions seem to be primarily responsible for the differences in the roll angle in the tetragonal structures but for both the roll and twist angles in the hexagonal structures. These results demonstrate that the majority of the observed helix base pair parameters for A-DNA octamers in crystals are affected by the crystal packing environment, while a few parameters, like propeller twist and base pair buckle display some base sequence dependence.

Base Composition↗
PubMed1995

Single-base sequencing and similarity comparisons.

A "single-base sequence" is a DNA sequence in which the identities and locations of bases of only one type have been determined. We present experimental procedures for single-base sequencing and describe the effective use of existing software (FASTA) in similarity comparisons of single-base sequences. We determined the theoretical and experimental minimum sequence lengths required for identification of a sequence within a large dataset and optimized the FASTA parameters for use in single-base similarity comparisons. Single-base sequences have been used to identify cDNAs occurring in a database. Single-base sequencing could be used to reduce the redundancy of "shot-gun sequencing."

Databases, Factual↗
PubMed2003

Numerical characterization and similarity analysis of DNA sequences based on 2-D graphical representation of the characteristic sequences.

Based on the classifications of the four nucleic acid bases, He and Wang reduced a DNA sequence to three binary sequences, which are called the characteristic sequences (J. Chem. Inf. Comput. Sci. 42 (2002) 1080). In this paper, we associate each characteristic sequence with a (b)L / (b)L matrix by giving a 2-D 'two horizontal lines' graphical representation, and thus obtain a 3-component vector with entries being the sums of the maximal and minimal eigenvalues of the (b)L / (b)L matrices. The introduced vector results in more simple characterizations and comparisons among the coding sequences of exon 1 of beta-globin gene of eleven different species.

Animals↗
PubMed1994

Human cysteine dioxygenase type I: primary structure derived from base sequencing of cDNA.

The base sequence of cDNA encoding the complete human liver cysteine dioxygenase type I (CDO-I; EC 1.13.11.20) message, and the derived amino-acid sequence are reported. CDO-I is encoded on a single mRNA species (approx. 1.5 kb). Human CDO-I clones were identified by screening a liver cDNA library, and inserts were isolated and sequenced. In addition, human liver total RNA was reverse-transcribed and CDO-I cDNA amplified by PCR using a modified poly-T primer and specific CDO-I primers to give a second source of sequencing template. The CDO-I message encodes a 200 amino-acid residue protein, the sequence of which has greater than 90% homology with the equivalent rat enzyme. The message was not expressed in a human hepatoma cell line (Hep G2).

Amino Acid Sequence↗
PubMed2003

Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing.

High-level resistance to multiple drugs is often detected by directly sequencing uncloned polymerase chain reaction products (population-based sequencing). It is not known, however, if this method of identifying mutations gives an accurate picture of individual viral genomes. To determine how often multidrug-resistant isolates consist of clones containing every mutation present in the population-based sequence, a mean of 2.8 molecular clones was sequenced from the plasma of 25 heavily treated persons whose population-based sequence contained multiple reverse transcriptase (RT) inhibitor resistance mutations (71 clones). The 25 population-based sequences contained a mean of 5.7 nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations and 1.2 nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations. The 71 clones contained a mean of 5.3 NRTI resistance mutations and 1.0 NNRTI resistance mutations. Sequences of clones closely resembled the population-based sequence: 36 (51%) clones had each of the RT inhibitor mutations present in the population-based sequence, 25 (35%) had all but 1 RT inhibitor mutation, 4 (6%) had all but 2 RT inhibitor mutations, 3 (4%) had all but 3 RT inhibitor mutations, and 3 (4%) had all but 4 RT inhibitor mutations. Phenotypic testing of 29 clones showed that most clones were resistant to nearly all NRTIs and that those with NNRTI resistance mutations were also resistant to multiple NNRTIs. These data show that in heavily treated persons, most RT inhibitor resistance mutations are present in the same viral genomes (colinear) and that multidrug resistance often occurs within individual clones as well as within virus populations.

Amino Acid Sequence↗
PubMed2005

HLA-DQB1 sequencing-based typing using newly identified conserved nucleotide sequences in introns 1 and 2.

Sequencing-based typing (SBT) human leukocyte antigen (HLA) class I and II genes should examine entire exon sequences where polymorphisms lie. Primers for the amplification of complete exons therefore anneal in introns and their design relies on accurate intron sequences being available. We decided to develop a SBT method for HLA-DQB1 using amplification primers which anneal in introns 1 and 2, yet the amount of intron sequence data previously available in databases was sparse. Therefore, we undertook a systematic sequencing of introns 1 and 2 using DNA from cell lines homozygous for DQB1. This study confirmed an earlier report that the non-coding regions of this gene are the most polymorphic seen in the human genome. Intron sequences within an allele group were largely identical, the exceptions being DQB1*0301 differing from other DQB1*03 allele groups and DQB1*0601 differing from all other DQB1*06 alleles. A retroviral Alu element, related to the AluYa5a2 subfamily, was identified uniquely inserted in intron 2 of DQB1*02 alleles. For the typing approach, six amplification primers were designed based on conserved allele group sequences covering all of the HLA DQB antigens, and two sequencing primers were also designed which anneal in intron 2. This method has proved to be very robust and has been used as part of a referral DNA sequencing service for a number of years.

Alleles↗
PubMed2004

MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.

A method is described for performing global alignment of noncoding DNA sequences based on an evolutionary model parameterized by the frequency distribution of lengths of insertion/deletion events (indels) and their rate relative to nucleotide substitutions. A stochastic hill-climbing algorithm is used to search for the most probable alignment between a pair of sequences or three sequences of known phylogenetic relationship. The performance of the procedure, parameterized according to the empirical distribution of indel lengths in noncoding DNA of Drosophila species, is investigated by simulation. We show that there is excellent agreement between true and estimated alignments over a wide range of sequence divergences, and that the method outperforms other available alignment methods.

Algorithms↗
PubMed2005

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array.

One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.

Base Sequence↗
PubMed1991

Nucleic acid sequence-based amplification.

Nucleic acid sequence-based amplification (NASBA) is a primer-dependent technology that can be used for the continuous amplification of nucleic acids in a single mixture at one temperature.

Base Sequence↗
PubMed2004

A large case-control study of cervical cancer risk associated with human papillomavirus infection in Japan, by nucleotide sequencing-based genotyping.

Using nucleotide sequencing-based genotyping, we conducted a case-control study to examine cervical cancer risk associated with human papillomavirus (HPV) infection in a Japanese population. A consensus primer pair was used to amplify DNA from the L1 region of HPV by polymerase chain reaction (PCR). By PCR, 311 of 356 patients with cervical cancer and 333 of 3249 control individuals were positive for HPV. By the direct sequencing of PCR products, nucleotide sequences of 30 genotypes were obtained. A high incidence of type 52 and a low incidence of type 16 were characteristic of the control group. Odds ratios were estimated for 18 genotypes. Types 71, 90, and 91, previously uncharacterized, were classified as low-risk genotypes, which is consistent with predictions made on the basis of phylogeny. The present study is the first large case-control study of its kind to use nucleotide sequencing-based genotyping.

Adult↗
PubMedDate not supplied

Analysis of similarity/dissimilarity of DNA sequences based on nonoverlapping triplets of nucleotide bases.

We consider a 6-D representation of triplets of nucleotide bases of DNA sequences. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the triplets derived from DNA sequences. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.

Animals↗
PubMed2003

Dynamic range of fluorescence detection and base-calling accuracy in DNA sequencer based on single-photon counting.

Recently, we developed a family of high-performance automated capillary DNA sequencing instruments based on a single-photon detection of fluorescently labeled DNA fragments. Our machines employ digital and broadband techniques, essential for achieving superior instrument sensitivity and dynamic range. In the present paper, we discuss limitations of the instrument's performance caused by the nonlinearity of single-photon detectors as well as methods for nonlinearity compensation which increase the detection dynamic range and base-calling accuracy.

Electronics↗
PubMed1989

The conformation and stability of ribonucleic acids: modeling base sequence effects in double stranded helices.

Base sequence effects within double stranded RNA oligomers of A and Z conformations have been studied by molecular modeling using a methodological approach specifically adapted to nucleic acids. Calculations on symmetric oligomers having homonucleotide or dinucleotide repeating base sequences show that sequence changes can produce modifications in overall conformation, influence the degree of internal hydrogen bonding and strongly affect stability.

Base Sequence↗
PubMed2003

Mono-allelic amplification of exons 2-4 using allele group-specific primers for sequence-based typing (SBT) of the HLA-A, -B and -C genes: preparation and validation of ready-to-use pre-SBT mini-kits.

Class I allelic typing based on sequencing is reliable, immutable and easy to analyse when only one allele is amplified using a specific mono-allelic technique. A strategy has been developed to selectively amplify exons 2, 3 and 4 of each allele of the three class I loci, previously identified by generic typing, in order to sequence these alleles from their intronic parts in only one direction. This procedure is based mainly on the polymorphism of exon 1 and intron 1 of the HLA-A, -B and -C genes with allele group-specific forward primers and locus-specific reverse primers so as to perform mono-allelic amplification in a 'One Step' pre-sequence-based typing (pre-SBT) PCR. The 5' polymorphism found at each locus is nevertheless not sufficient to discriminate all allelic combinations. Hence exon 2 and exon 3 polymorphism had to be used in a 'Two Step' pre-SBT PCR method to selectively amplify the two alleles in the 1.8%, 7.6% and 0.9% of unresolved combinations found in our laboratory for, respectively, the HLA-A, -B and -C loci. Preparation and validation of 'ready-to-use' aliquots of primer-mixes, pre-SBT buffer and sets of Dye terminator reaction mixtures containing locus-specific intronic primers makes the procedure easy and efficient. The SBT method is the only allelic typing technique used in our laboratory (to date, 742 HLA-A*, 802 HLA-B* and 615 HLA-Cw* alleles have been sequenced) and our successful participation in the national and international quality controls of 4 years ago testifies to the accuracy of the results.

DNA Primers↗