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At least 379 records · Page 21Linked to original sources
PubMed2003

Sequence change and phylogenetic signal in muscoid COII DNA sequences.

The complete DNA sequence of the mtDNA cytochrome oxidase II gene from house fly, Musca domestica, face fly, Musca autumnalis, stable fly, Stomoxys calcitrans, horn fly, Haematobia irritans, and black garbage fly, Hydrotaea aenescens, are reported. The nucleotide sequence codes for a 229 amino acid peptide. The COII sequence is A + T rich (74.1%), with up to 12.3% nucleotide and 8.4% amino acid divergence among the five taxa. Of the 688 nucleotides encoding for the gene, 135 nucleotide sites (19.6%) are variable, and 55 (8.0%) are phylogenetically informative. A phylogenetic analysis using three calliphorids as the outgroup taxa, indicates that the two haematophagus species, horn fly and stable fly, form a sister group.

Amino Acid Sequence↗
PubMed2001

DNA sequencing and genotyping by transcriptional synthesis of chain-terminated RNA ladders and MALDI-TOF mass spectrometry.

Sets of RNA ladders can be synthesized by transcription of a bacteriophage-encoded RNA polymerase using 3'-deoxynucleotides as chain terminators. These ladders can be used for sequencing of DNA. Using a nicked form of phage SP6 RNA polymerase in this study substantially enhanced yields of transcriptional sequencing ladders. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of chain-terminated RNA ladders allowed DNA sequence determination of up to 56 nt. It is also demonstrated that A-->G and C-->T variations in heterozygous and homozygous samples can be unambiguously identified by the mass spectrometric analysis. As a step towards single-tube sequencing reactions, alpha-thiotriphosphate nucleotide analogs were used to overcome problems caused by chain terminator-independent, premature termination and by the small mass difference between natural pyrimidine nucleotides.

Base Sequence↗
PubMed2006

A weighted measure for the similarity analysis of DNA sequences.

Here we propose a weighted measure for the similarity analysis of DNA sequences. It is based on LZ complexity and (0,1) characteristic sequences of DNA sequences. This weighted measure enables biologists to extract similarity information from biological sequences according to their requirements. For example, by this weighted measure, one can obtain either the full similarity information or a similarity analysis from a given biological aspect. Moreover, the length of DNA sequence is not problematic. The application of the weighted measure to the similarity analysis of beta-globin genes from nine species shows its flexibility.

Animals↗
PubMed1996

Location, DNA sequence and transcriptional analysis of the DNA polymerase gene of orf virus.

Degenerate oligonucleotides representing conserved regions of various DNA polymerases hybridized to a region located 26 kb from the left end of the orf virus (OV) strain NZ-2 genome. DNA sequence analysis of this region revealed a 3024 bp open reading frame able to encode a protein with 56 percent amino acid identity to the DNA polymerase of vaccinia virus (VAC) and with significant homology to other DNA polymerases. Early transcripts derived from the open reading frame were detected in RNA purified from OV-infected cells, and 5' ends were mapped to a region 8-19 nt downstream from an A/T-rich sequence that resembles VAC early promoters. Unlike the VAC gene, the OV DNA polymerase makes almost exclusive use of G/C coding options. Attempts to substitute the activity of the OV DNA polymerase for its VAC counterpart were unsuccessful. This may indicate that the OV DNA polymerase is incompatible with VAC accessory proteins.

Amino Acid Sequence↗
PubMed1983

Specific association of repetitive DNA sequences with major histocompatibility genes.

The DNA sequence organization of a 17.8-kilobase segment of porcine DNA, containing a functional major histocompatibility (MHC) gene, has been studied. The DNA flanking the MHC gene contains at least 10 distinct repetitive DNA sequence elements, each of which occurs only once within the 17.8-kilobase DNA segment. Their reiteration frequencies in the genome range from 10(2) to 10(4). The genomic organization of seven of these sequence elements has been examined; all are interspersed with other, unrelated DNA sequences. These seven repeated sequences are not generally associated in the genome. However, they appear to be nonrandomly linked in MHC-associated regions of the genome: at least two additional DNA segments containing MHC-homologous DNA also contain sequences homologous to DNA fragments bearing the seven different repeats. Of the seven sequences, four can be detected in splenic total RNA. These results suggest that these repeated elements are specifically associated with the MHC locus.

Animals↗
PubMed1993

An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms.

A data set consisting of DNA sequences from a large-scale shotgun DNA cloning and sequencing project has been collected and posted for public release. The purpose is to propose a standard genomic DNA sequencing data set by which various algorithms and implementations can be tested. This set of data is divided into two subsets, one containing raw DNA sequence data (1023 clones) and the other consisting of the corresponding partially refined or edited DNA sequence data (820 clones). Suggested criteria or guidelines for this data refinement are presented so that algorithms for preprocessing and screening raw sequences may be developed. Development of such preprocessing, screening, aligning, and assembling algorithms will expedite large-scale DNA sequencing projects so that the complete unambiguous consensus DNA sequences will be made available to the general research community in a quicker manner. Smaller scale routine DNA sequencing projects will also be greatly aided by such computational efforts.

Algorithms↗
PubMed2005

Analysis of sequence variation in Gnathostoma spinigerum mitochondrial DNA by single-strand conformation polymorphism analysis and DNA sequence.

Morphological variations were observed in the advance third stage larvae of Gnathostoma spinigerum collected from swamp eel (Fluta alba), the second intermediate host. Larvae with typical and three atypical types were chosen for partial cytochrome c oxidase subunit I (COI) gene sequence analysis. A 450 bp polymerase chain reaction product of the COI gene was amplified from mitochondrial DNA. The variations were analyzed by single-strand conformation polymorphism and DNA sequencing. The nucleotide variations of the COI gene in the four types of larvae indicated the presence of an intra-specific variation of mitochondrial DNA in the G. spinigerum population.

Animals↗
PubMedDate not supplied

Some notes on 2-D graphical representation of DNA sequence.

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this paper, we presented a novel graphical representation of DNA sequences by taking four special vectors in 2-D Cartesian coordinate system to represent the four nucleic acid bases in DNA sequences, so that a DNA sequence is denoted on a plane by a directed walk. It is shown that the new graphical representation of DNA sequences has lower or nondegeneracy.

DNA↗
PubMed2001

DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.

We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, 'jumping PCR', i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than approximately 0.1% even under the unlikely scenario where each amplification starts from a single template molecule.

Animals↗
PubMed1990

Identification and DNA sequence of the Shope fibroma virus DNA topoisomerase gene.

The Shope fibroma virus (SFV) DNA topoisomerase gene has been identified and mapped to the BamHI D fragment near the midpoint of the genome. The DNA sequence of the SFV BamHI S fragment together with the contiguous BamHI-ClaI subfragment of BamHI D which encompasses the topoisomerase gene and two flanking genes has been determined and analyzed. Both the SFV DNA topoisomerase and the two flanking genes are closely related in terms of sequence and spatial organization to the homologous sequences from the midpoint of the vaccinia virus genome, indicating that these proteins are conserved not only in their sequence but also by position within the poxvirus genome. To confirm the assignment of the SFV gene, the putative SFV DNA topoisomerase has been expressed as an active fusion protein in Escherichia coli and this system should be useful in the analysis of topoisomerase function following the introduction of targeted mutations into the topoisomerase gene. The results of this work shed further light on the evolutionary relationship of the different poxvirus genera and indicate that central unique regions of the poxvirus genomes contain many of the essential viral genes and are thus highly conserved.

Amino Acid Sequence↗
PubMed2006

Clustering DNA sequences by feature vectors.

We represent all DNA sequences as points in twelve-dimensional space in such a way that homologous DNA sequences are clustered together, from which a new genomic space is created for global DNA sequences comparison of millions of genes simultaneously. More specifically, basing on the contents of four nucleotides, their distances from the origin and their distribution along the sequences, a twelve-dimensional vector is given to any DNA sequence. The applicability of this analysis on global comparison of gene structures was tested on myoglobin, beta-globin, histone-4, lysozyme, and rhodopsin families. Members from each family exhibit smaller vector distances relative to the distances of members from different families. The vector distance also distinguishes random sequences generated based on same bases composition. Sequence comparisons showed consistency with the BLAST method. Once the new gene is discovered, we can compute the location of this new gene in our genomic space. It is natural to predict that the properties of this new gene are similar to the properties of known genes that are locating near by. Biologists can do various experiments to test these properties.

DNA↗
PubMed1986

Detection of amplified DNA sequences in gastric cancers by a DNA renaturation method in gel.

A DNA renaturation method in gel was used to detect amplified DNA fragments in eight gastric cancer cell lines, KATO-III, OKAJIMA, SCH, MKN1, MKN7, MKN28, MKN45 and MKN74 cells, and tissues of three metastases of gastric cancers to lymph nodes. There were amplified DNA sequences in three gastric cancer cell lines. Judging from the intensities of the bands, HindIII-digested DNA fragments were amplified several hundred times in the KATO-III and MKN7 cell lines. DNA from OKAJIMA cell line contained multiple bands with less intensity. KATO-III cells were found to contain a homogeneously staining region in chromosome 11.

Base Sequence↗
PubMed1996

Thermal cycle dideoxy DNA sequencing.

Thermal cycle dideoxy DNA sequencing eliminates the requirements for independent primer annealing and double-stranded DNA denaturation steps. The method enables sequencing from nanogram amounts of DNA from double-stranded and single-stranded PCR products, and plasmid or phage DNA templates. Thermal cycle sequencing also enables direct sequencing from bacterial colonies or phage plaques. Protocols using the Vent exo- DNA polymerase, helpful suggestions, and a troubleshooting guide are also presented.

Dideoxynucleosides↗
PubMed1998

Searching DNA databases for similarities to DNA sequences: when is a match significant?

MOTIVATION: Searching DNA sequences against a DNA database is an essential element of sequence analysis. However, few systematic studies have been carried out to determine when a match between two DNA sequences has biological significance and this is limiting the use that can be made of DNA searching algorithms. RESULTS: A test set of DNA sequences has been constructed consisting of artificially evolved and real sequences. This set has been used to test various database searching algorithms (BLAST, BLAST2, FASTA and Smith-Waterman) on a subset of the EMBL database. The results of this analysis have been used to determine the sensitivity and coverage of all of the algorithms. Guidelines have been produced which can be used to assess the significance of DNA database search results. The Smith-Waterman algorithm was shown to have the best coverage, but the worst sensitivity, whereas the default BLASTN algorithm (word length set to 11) was shown to have good sensitivity, but poor coverage. A sensible compromise between speed, sensitivity and coverage can be obtained using either the FASTA or BLAST (word length set to 6) algorithms. However, analysis of the results also showed that no algorithm works well when the length of the probe sequence is <200 bases. In general, matches can accurately be identified between coding regions of DNA sequences when there is >35% sequence identity between the corresponding proteins. Searching a DNA sequence against a DNA sequence database can, therefore, be a useful tool in sequence analysis. AVAILABILITY: The test sets used are available via anonymous ftp from mbisg2.sbc.man.ac.uk in the directory /pub/cabios/testdata/ CONTACT: I.Anderson@stud.man.ac.uk; abrass@man.ac.uk

Algorithms↗
PubMed1999

Statistical analysis of DNA sequencing data (1): accuracy test of DNA data by partial re-sequencing.

To qualify DNA data, we have developed a statistical method of deciding whether the DNA data has an acceptable accuracy in sequencing process. The method is to test the probability of sequencing errors, based on partial re-sequencing. The method was successfully applied to a yeast mitochondrial DNA which is previously sequenced (1). The analysis indicates that the entire sequence is very accurate although we found one base change error on the ND1 gene sequence data by a partial re-sampling. This method is applicable to any DNA data.

Chromosome Mapping↗
PubMed1997

Transfection of the inner cell mass and lack of a unique DNA sequence affecting the uptake of exogenous DNA by sperm as shown by dideoxy sequencing analogues.

PURPOSE: The purpose of this study was to determine whether exogenous DNA internalized into blastocysts after transference from DNA-carrier sperm are localized at the inner cell mass or trophoblast cells and to identify differences in uptake of exogenous DNA fragments by sperm due to unique DNA sequences. METHODS: Mouse blastocysts at the hatching stage were exposed to migrating human sperm cells carrying exogenous DNA fragments synthesized from the E6-E7 conserved gene regions of human papillomavirus (HPV) types 16 and 18. After an interaction period of 2 hr, the transfected blastocysts were washed several times to remove extraneous sperm and the blastocysts were dissected into groups of cells derived from the inner cell mass and trophoblasts. The cells were analyzed by polymerase chain reaction (PCR) for the presence of HPV DNA fragments. In the second part of the experiment, thawed donor (N = 10) sperm cells were pooled, washed, and divided into two fractions. The first (control) fraction was added with formalin and further divided and added with a 35S-radiolabeled G, A, T, or C sequencing mixture. The second fraction was similarly treated but the formalin step was omitted from the treatment. After an hour of incubation at 37 degrees C, the sperm specimens were washed several times by centrifugation and DNA extracted by the GeneReleaser method. The extracted DNA were processed on sequence gels, and the autoradiographs analyzed. RESULTS: Mouse blastocysts transfected by carrier sperm with DNA from HPV types 16 and 18 showed localization of the HPV DNA to both the inner cell mass and trophoblast cells. Negative controls consisting of untreated human sperm and untreated mouse blastocysts did not reveal any evidence of HPV DNA. The positive sperm control generated expected DNA fragments from HPV types 16 and 18. In the second experiment, the intensities of the DNA fragments in the G, A, T, and C columns from low to high molecular weights were not different from the positive control bands. Band intensities of the four sequencing columns were similar. Formalin pretreatment of the sperm inhibited uptake of the DNA fragments from the smallest to the largest DNA molecules. CONCLUSIONS: Exogenous DNA taken into blastocysts are localized to both the inner cell mass and trophoblast cells. Only live sperm exhibited the capacity to carry various sizes of exogenous DNA, suggesting the involvement of active cell membrane mechanism in the transference process. The results showed that DNA fragments terminating in any of the four nucleotides were equally taken up by the sperm cell. Fragments of DNA produced by the sequencing reaction failed to identify a unique DNA sequence that would facilitate or inhibit the sperm from taking up exogenous DNA.

Animals↗
PubMed2000

Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons.

This study examines sequence divergence in three spacer regions of the ribosomal DNA (rDNA) cistron, to test the hypothesis of unequal mutation rates. Portions of two transcribed spacers (ITS-1 and 5' ETS) and the non-transcribed spacer (NTS) or intergenic spacer (IGS) formed the basis of comparative analyses. Sequence divergence was measured both within an individual lake trout (Salvelinus namaycush) and among several related salmonid species (lake trout; brook trout, Salvelinus fontinalis; Arctic char, Salvelinus alpinus; Atlantic salmon, Salmo salar; and brown trout, Salmo trutta). Despite major differences in the length of the rDNA cistron within individual lake trout, minimal sequence difference was detected among cistrons. Interspecies comparisons found that molecular variation in the rDNA spacers did not conform to the predicted pattern of evolution (ITS spacers<ETS spacers<IGS). Specifically, the IGS contains a region that appears to be as highly, or more conserved than the ITS-1.

Amino Acid Sequence↗