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At least 217 records · Page 12Linked to original sources
PubMed1986

A DNA sequence analysis program for the Apple Macintosh.

This paper describes a new set of programs for analyzing DNA sequences using the Apple Macintosh computer, a computer ideally suited for this kind of analysis. Because of the Macintosh interface and the availability of high quality software-only speech synthesis, these programs are truly easy to use. Instead of typing in commands, the user directs the program by making selections with the mouse, thereby eliminating most typographical and syntax errors. Output options are selected by "pressing buttons" and then clicking "OK" with the mouse. DNA sequences are confirmed by having the program speak them. The high resolution graphics on the Macintosh not only allow for explanatory diagrams to be used to aid in deciding on input parameters, but can be used to produce slides for presentations and figures for papers. Because of the clipboard and the ability of the Macintosh to readily share data among different applications, data can be saved for use directly in word processing documents (e.g. manuscripts).

Animals↗
PubMed1982

A convenient and adaptable package of DNA sequence analysis programs for microcomputers.

We describe a package of DNA data handling and analysis programs designed for microcomputers. The package is convenient for immediate use by persons with little or no computer experience, and has been optimized by trial in our group for a year. By typing a single command, the user enters a system which asks questions or gives instructions in English. The system will enter, alter, and manage sequence files or a restriction enzyme library. It generates the reverse complement, translates, calculates codon usage, finds restriction sites, finds homologies with various degrees of mismatch, and graphs amino acid composition or base frequencies. A number of options for data handling and printing can be used to produce figures for publication. The package will be available in ANSI Standard FORTRAN for use with virtually any FORTRAN compiler.

Amino Acid Sequence↗
PubMed2004

Phylogeny of the multivalvulidae (Myxozoa: Myxosporea) based on comparative ribosomal DNA sequence analysis.

Fish parasites of the Multivalvulida (Myxozoa, Myxosporea) are widespread and can be associated with mortality or poor flesh quality in their commercially important marine hosts. Traditional classifications divide members of this order into families based on spore valve and polar capsule numbers. Analyses of the small-subunit (SSU) ribosomal DNA (rDNA) sequences from all representative families in the order (Trilosporidae, Kudoidae, Pentacapsulidae, Hexacapsulidae, and Septemcapsulidae) indicate that a revision of the taxonomy and nomenclature is warranted. In our phylogenetic analysis of (SSU and large subunit) rDNA sequences, members of Pentacapsula, Hexacapsula, and Septemcapsula root within a clade of Kudoa species with Unicapsula (Trilosporidae) as an outlier to these genera. Therefore, we propose to synonymize Pentacapsulidae, Hexacapsulidae, and Septemcapsulidae with Kudoidae alter the diagnosis of Kudoidae and Kudoa to accommodate all marine myxozoan parasites having 4 or more shell valves and polar capsules.

Animals↗
PubMed1992

DNA sequence analysis of mutations induced by melphalan in the CHO aprt locus.

In previous work, we established that treatment with melphalan (L-phenylalanine mustard) produced a predominance of A.T-->T.A transversions in the Simian virus 40 (SV40)-based shuttle vector pZ189 during replication in human 293 cells. Mutations were induced with varying doses (4-12 microM) melphalan in the aprt gene of the hemizygous Chinese hamster ovary (CHO) cell line D422 to determine whether a similar mutation spectrum would be observed in an endogenous gene. DNA sequence alterations were determined for 39 spontaneous and 41 melphalan-induced independent mutant clones. Other than a predominance of transversions in both systems, the spectrum of melphalan-induced aprt mutations bears little resemblance to the spectrum observed in the supF gene of the shuttle plasmid pZ189. In aprt, mutations at G.C base pairs (bp) predominated (29 of 41 base substitutions). Significantly enhanced mutagenesis was observed at 5' G-G-C 3' and 5' G-G-C-C 3' sites in the aprt gene. Almost half of the melphalan-induced base substitutions occurred at 5' G-N-C 3' sequences, which are believed to be potential interstrand crosslink sites.

Adenine Phosphoribosyltransferase↗
PubMed1996

Molecular phylogeny of grey mullets based on mitochondrial DNA sequence analysis: evidence of a differential rate of evolution at the intrafamily level.

The phylogeny of the grey mullets is considered problematic both at the intra- and interfamily level. Such a difficulty arises from the highly homogeneous morphology displayed by this group of fish and, consequently, from the paucity of the key morphological characters suitable to address their phylogeny and evolution. In the present work, we have approached the phylogenetic and evolutionary relationships of seven species of Mugilidae, six of which from the Mediterranean Sea, on the basis of the DNA sequences of two mitochondrial genes (cytochrome b and 12S rRNA). Despite the morphological homogeneity exhibited by the taxa considered, the two species of the genus Mugil (M. cephalus and M. curema) showed a remarkable genetic divergence compared to all the other members of the family. The relative rate test revealed a significantly higher rate of evolution along the Mugil lineage.

Animals↗
PubMedDate not supplied

Ribosomal DNA sequence analysis shows that the basidiomycete C30 belongs to the genus Trametes.

The basidiomycete C30 was considered as an isolate of a population of Marasmius quercophilus collected on evergreen oak litter from the Mediterranean forest. Recent phenotypic studies have clearly shown that it differs from newly characterized M. quercophilus isolates. Subsequent analysis of laccase genes revealed that C30 sequences are similar to laccase encoding sequences from organisms belonging to the polyporoid clade. Comparison of sequences of the C30 ITS regions, including 5.8S rDNA, with those found in databanks confirmed that C30 is not a Marasmius. Finally, 25S rDNA analysis revealed that C30 is closely related to the Coriolaceae and, in particular, to Trametes trogii.

Basidiomycota↗
PubMed1994

DNA sequence analysis of spontaneous and gamma-radiation (anoxic)-induced lacId mutations in Escherichia coli umuC122::Tn5: differential requirement for umuC at G.C vs. A.T sites and for the production of transversions vs. transitions.

Escherichia coli umuC122::Tn5 cells were gamma-irradiated (137Cs, 750 Gy, under N2), and lac-constitutive mutants were produced at 36% of the wild-type level (the umuC strain was not deficient in spontaneous mutagenesis, and the mutational spectrum determined by sequencing 263 spontaneous lacId mutations was very similar to that for the wild-type strain). The specific nature of the umuC strain's partial radiation mutability was determined by sequencing 325 radiation-induced lacId mutations. The yields of radiation-induced mutation classes in the umuC strain (as a percentage of the wild-type yield) were: 80% for A.T-->G.C transitions, 70% for multi-base additions, 60% for single-base deletions, 53% for A.T-->C.G transversions, 36% for G.C-->A.T transitions, 25% for multi-base deletions, 21% for A.T-->T.A transversions, 11% for G.C-->C.G transversions, 9% for G.C-->T.A transversions, and 0% for multiple mutations. Based on these deficiencies and other factors, it is concluded that the umuC strain is near-normal for A.T-->G.C. transitions, single-base deletions and possibly A.T-->C.G transversions; is generally deficient for mutagenesis at G.C sites and for transversions, and is grossly deficient in multiple mutations. Damage at G.C sites seems more difficult for translesion DNA synthesis to bypass than damage at A.T sites, and especially when trying to produce a transversion. The yield of G.C-->A.T transitions in the umuC strain (36% of the wild-type level) argues that abasic sites are involved in no more than 64% of gamma-radiation-induced base substitutions in the wild-type strain. Altogether, these data suggest that the UmuC and UmuD' proteins facilitate, rather than being absolutely required for, translesion DNA synthesis; with the degree of facilitation being dependent both on the nature of the noncoding DNA damage, i.e., at G.C vs. A.T sites, and on the nature of the misincorporated base, i.e., whether it induces transversions or transitions.

Bacterial Proteins↗
PubMed2001

Identification of Candida dubliniensis, based on ribosomal DNA sequence analysis.

Differentiation of Candida albicans and the recently described C. dubliniensis has proven difficult due to the high degree of phenotypic similarity of these species. The present study examines sequence variations in the ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions of C. albicans (n = 5) and C. dubliniensis (n = 7) strains, with a view to identifying sequence differences that would enable consistent differentiation of these two species by restriction fragment length polymorphism (RFLP) analysis. The ITS1 and ITS2 regions, together with the entire 5.8S rRNA gene of the strains, were amplified by the polymerase chain reaction (PCR), using primers ITS1 and ITS4, PCR products from both C. albicans and C. dubliniensis were of similar size (around 540 bp); however, sequence analysis revealed over 20 consistent base differences between the products of the two species. On the basis of sequence variation, the restriction enzyme MspA1 I was selected and used to differentiate the PCR products of C. albicans and C. dubliniensis by RFLP analysis. MspA1 I yielded two discernible fragments from C. albicans PCR products, whilst those from C. dubliniensis appeared undigested, thereby providing an approach to differentiate the two species.

Candida↗
PubMed2006

Scale-up development of high-performance polymer matrix for DNA sequencing analysis.

Linear polyacrylamide (LPA) has been widely used as a replaceable separation matrix in CE. An increase in the molecular weight of the separation medium favors the separation of larger DNA fragments. In order to obtain ultrahigh-molecular-weight (UHMW) LPA, a "frozen" method was developed to synthesize the LPA homopolymer. This approach has three major advantages when compared with other existing routes of LPA synthesis: (i) long LPA chains could be obtained easily, with their average molecular weight (MW) being in the high 10 MDa range; (ii) the desired MW could be adjusted over a broad range by controlling the temperature and the concentration of initiators during synthesis; (iii) the product solution contains only a tiny amount of impurity besides the solvent and LPA. Both static and dynamic laser light scattering measurements were carried out to characterize the synthesized LPA in the buffer solution. The DNA sequencing matrix prepared from LPA using this method was studied and the results were compared with the newly developed commercial product POP7 from Applied Biosystems. It should be noted that this approach can be applied to synthesize other water-soluble polymers, resulting in UHMW products because the chain transfer constant is smaller at lower temperatures.

Acrylic Resins↗
PubMed1999

[p53 gene mutation determined by single-strand conformational polymorphism and DNA sequencing analysis in pleomorphic adenoma of salivary gland].

OBJECTIVE: To detect p53 exon 6 mutation pattern in pleomorphic adenoma of salivary gland. METHODS: Single-strand conformational polymorphism (SSCP) and DNA sequecing were used. RESULTS: SSCP analysis showed that 6 of 11 cases with SSCP positive were exon 6 abnormal. Comparison of the SSCP results with DNA sequecing, 4 cases with p53 exon 6 mutations were SSCP positive. Mutation pattern included base substitution (point mutation, G-->T, T-->G) and frame-shift mutation (base insertion and base loss). CONCLUSION: Poly-codon and poly-pattern mutations appeared in p53 exon 6. PCR-SSCP was a convenient method to detecte gene mutation.

Adenoma, Pleomorphic↗
PubMed2001

Visual Cloning 2000: a DNA sequence analysis program.

VC2000 is a recommendable, easy-to-use and affordable program suited particularly to plot maps of both plasmids and linear DNA fragments for the documentation of cloning procedures. It comes with basic tools for sequence analysis that assist this major utility. A special feature of the program is the integration of web-based tools, providing additional analytical power and flexibility. In this way the user is supplied with the latest versions of these applications.

Cloning, Molecular↗
PubMed1990

gm: a practical tool for automating DNA sequence analysis.

The gm (gene modeler) program automates the identification of candidate genes in anonymous, genomic DNA sequence data. gm accepts sequence data, organism-specific consensus matrices and codon asymmetry tables, and a set of parameters as input; it returns a set of models describing the structures of candidate genes in the sequence and a corresponding set of predicted amino acid sequences as output, gm is implemented in C, and has been tested on Sun, VAX, Sequent, MIPS and Cray computers. It is capable of analyzing sequences of several kilobases containing multi-exon genes in less than 1 min execution time on a Sun 4/60.

Algorithms↗
PubMed1989

Osteonectin promoter. DNA sequence analysis and S1 endonuclease site potentially associated with transcriptional control in bone cells.

To understand the basis of osteonectin (SPARC) transcriptional regulation, we have isolated a bovine genomic clone (lambda Og15) encoding exon 1 and 15 kilobase pairs (kb) of flanking DNA. Direct RNA sequencing of the 5' end of the osteonectin message showed it contained a sequence identical to that of a 2.4-kb EcoRI-BamHI fragment located midway in the clone lambda Og15. The results indicate exon 1 is located 10 kb away from exon 2 in the bovine genome. The DNA sequence unit CCTG is repeated five times in exon 1 which is composed exclusively of untranslated sequence. Sequence analysis of the 5'-flanking DNA revealed the presence of many regulatory motifs including a "GC" box with four overlapping SP1 consensus sequences. Immediately downstream from the GC box is a 72-base pair purine-rich stretch composed primarily of direct repeats of the sequence motifs GGGGA and GGA (GAGA box). Digestion of the flanking DNA in vitro with S1 endonuclease showed a site for the enzyme at position -55 which is just 3' to the GAGA box. Chimeric chloramphenicol acetyltransferase constructs were prepared containing the S1-sensitive site and showed substantial transcriptional activity in UMR-106 and fetal and adult human bone cells which are known to be high producers of the protein. The results indicate a potential regulatory activity of the S1 site in osteonectin gene activation.

Animals↗
PubMed2000

Diversity in the yeast Cryptococcus albidus and related species as revealed by ribosomal DNA sequence analysis.

Evidence accumulated from studies based on physiological, biochemical, and molecular characteristics has pointed to the heterogeneity of the ubiquitous anamorphic basidiomycetous yeast species Cryptococcus albidus (Saito) Skinner, with its current varieties and synonyms. The taxonomic status of this species has not been reappraised because different studies, mostly involving limited numbers of strains, have not been integrated. To assess species diversity within the clade containing Cryptococcus albidus and other phylogenetically related Cryptococcus and Filobasidium species, we determined ribosomal DNA (rDNA) sequences of 69 strains from the 5' end of the 26S gene, D1/D2 region, and in some cases, the non-coding ITS2 region. Analysis of the sequence data together with available physiological, biochemical, and molecular characteristics, showed the segregation of C. albidus into at least 12 species, leading to the elevation of former varieties to the rank of species (C. aerius, C. diffluens), the reinstatement of synonyms (C. liquefaciens, C. terricola), and the proposal of new species (C. arrabidensis, C. chernovii, C. cylindricus, C. oeirensis, C. phenolicus, C. saitoi, C. uzbekistanensis, C. wieringae). The overall analyses of the results argue in favour of the use of rDNA sequence data to improve species delineation when integrated with other available physiological and molecular characteristics.

Basidiomycota↗
PubMed2004

DNA sequence analysis of monoamine oxidase B gene coding and promoter regions in Parkinson's disease cases and unrelated controls.

The allele G of the intron 13 G/A polymorphism of the monoamine oxidase B gene (MAO-B) has been associated with Parkinson's disease (PD) in several studies. Apart from a potential direct effect on splicing processes, the association of this intronic polymorphism with PD is due possibly to linkage disequilibrium with other mutations in the coding or promoter regions of the gene. We addressed this latter hypothesis by determining the DNA sequence of the entire MAO-B coding region comprising 15 exons and partial intronic sequences flanking each exon, in 33 cases with idiopathic PD and 38 unrelated controls. The promoter region of MAO-B gene up to base -1,369 from ATG (start point of mRNA translation) was also sequenced to identify variants with potential functional effects on gene transcription. In the promoter region, a new polymorphism consisting of a C to T single base change was detected in position -1,114 from ATG, with an allelic frequency of 3.5%, but it was not associated with PD risk. No commonly occurring (>10%) polymorphisms were found in the exons or the intronic sequences flanking the exons, although several rare variants were detected in the coding and promoter regions.

Aged↗
PubMed1993

DNA sequence analysis of the YCN2 region of chromosome XI in Saccharomyces cerevisiae.

A 6.8 kbp DNA fragment localized to the left arm of chromosome XI from Saccharomyces cerevisiae was sequenced and analysed (EMBL accession no. X69765). Two genes involved in protein phosphatase activity were identified: YCN2 and an open reading frame encoding a protein that shares 46% amino acid identity with the sds22+ protein from Schizosaccharomyces pombe. A comparison of the genomic YCN2 sequence with the published cDNA sequence suggests the presence of an intron near the 5' end of the gene. Further sequence analysis suggests the presence of three additional genes near YCN2: a mitochondrial acyl-carrier protein, a gene encoding a putative hydrophobic protein, and a new gene coding for a tRNA(Leu) (UAA) isoacceptor located near a delta sequence.

Acyl Carrier Protein↗
PubMed1993

Evolution of the dec-1 eggshell locus in Drosophila. II. Intraspecific DNA sequence analysis reveals length mutations in a repetitive region in D. melanogaster.

The dec-1 eggshell gene in Drosophila melanogaster encodes follicle cell proteins required for proper eggshell assembly. As shown by Southern and Northern analyses the dec-1 gene occurs in four alleles (Fc1-4) among wild-type strains. Its second exon has a distinct feature in the form of 12 repeats with 78-91 nucleotides; the first five show nearly 100% homology. DNA sequence comparison of the repeated region of the alleles revealed that the length polymorphisms are caused by changes in the numbers of the first five repeats. The results suggest that the alleles have been generated by unequal intragenic crossing-over and/or slippage during DNA replication and that the allelic length variants have arisen independently. The possibility that the most common allele, FC1, has a selective advantage over the other alleles is discussed.

Alleles↗