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PubMed1982

MAXAMIZE. A DNA sequencing strategy advisor.

The MAXAMIZE advisory system determines from user-provided restriction maps an optimal strategy to do nucleotide sequencing by methods involving end-labeled fragments. The maps may be either simple linear restriction maps of fragments or complex circular maps including restriction sites of a vector. The whole system is interactive and is written in the Genetic English language provided by the GENESIS System, a molecular genetics knowledge representation and manipulation package. In addition, MAXAMIZE provides bookkeeping facilities for sequencing and offers advise on how to verify the newly obtained sequence data.

Base Sequence↗
PubMed2005

Fast and cheap genome wide haplotype construction via optical mapping.

We describe an efficient algorithm to construct genome wide haplotype restriction maps of an individual by aligning single molecule DNA fragments collected with Optical Mapping technology. Using this algorithm and small amount of genomic material, we can construct the parental haplotypes for each diploid chromosome for any individual. Since such haplotype maps reveal the polymorphisms due to single nucleotide differences (SNPs) and small insertions and deletions (RFLPs), they are useful in association studies, studies involving genomic instabilities in cancer, and genetics, and yet incur relatively low cost and provide high throughput. If the underlying problem is formulated as a combinatorial optimization problem, it can be shown to be NP-complete (a special case of K-population problem). But by effectively exploiting the structure of the underlying error processes and using a novel analog of the Baum-Welch algorithm for HMM models, we devise a probabilistic algorithm with a time complexity that is linear in the number of markers for an epsilon-approximate solution. The algorithms were tested by constructing the first genome wide haplotype restriction map of the microbe T. pseudoana, as well as constructing a haplotype restriction map of a 120 Mb region of Human chromosome 4. The frequency of false positives and false negatives was estimated using simulated data. The empirical results were found very promising.

Algorithms↗
PubMed1997

Integrated map of the Schizosaccharomyces pombe genome.

A restriction map of the entire Schizosaccharomyces pombe genome was constructed using two restriction enzymes (BamHI and PstI) that recognize 6 bp. The restriction map contains 420 minimally overlapping clones (miniset) and has 22 gaps. We located 126 genes, marker fragments of DNA (NotI and SfiI linking clones), and 36 transposable elements by hybridization to unique restriction fragments.

Base Sequence↗
PubMed1981

Restriction endonuclease map of phage group 2 Staphylococcus aureus exfoliative toxin plasmid.

A restriction endonuclease map of the phage group 2 Staphylococcus aureus exfoliative toxin plasmid pRW001 was constructed. The orientation of the restriction endonuclease fragments was determined by a series of single and double enzyme digestions. The location of the deletions found in pRW002, a naturally occurring deletion mutant of the exfoliative toxin plasmid, was determined by comparing the restriction endonuclease fingerprints of the two plasmids. This physical map provided a means for comparing other insertion or deletion mutants of the exfoliative toxin plasmid.

Bacterial Toxins↗
PubMed1995

A restriction enzyme map of the sex-linked late-feathering locus of chickens.

A 34-kb restriction endonuclease map of the region associated with an endogenous virus integration site and K, the gene that confers sex-linked late-feathering (LF) in chickens, is presented. Hybridizations of genomic blots of DNA from early-feathering and LF White Leghorns indicated that the region also contains additional repetitive elements upstream from a chicken repetitive (CR1) element. This extended map and the probes described should be useful in identifying the molecular alterations associated with this locus.

Alpharetrovirus↗
PubMed1993

Genomic cloning and restriction site mapping of a porcine adenovirus isolate: demonstration of genomic stability in porcine adenovirus.

Restriction endonuclease maps were constructed for the genome of a porcine adenovirus (PAV), NADC-1, which was isolated in 1972 from an adult swine. Genomic DNA libraries of NADC-1 Bam HI, Eco RI/Bam HI, and Sph I fragments were cloned into pUC-18. Using the cloned NADC-1 Bam HI and Eco RI/Bam HI fragments as probes, Southern blot hybridizations were performed to human adenovirus 2 (Ad-2) restriction fragments to determine the left-to-right orientation of the Bam HI and Eco RI/Bam HI fragments. Genomic NADC-1 DNA was cleaved with ten restriction endonucleases (RE). Using cloned NADC-1 genomic fragments as probes in Southern blot hybridizations, an RE site map was constructed. Nucleotide sequencing of four clones confirmed several RE sites. The size of the NADC-1 genome was determined to be approximately 32 kbp. The size of Hind III, Xba I, Sma I, Eco RI, Bam HI, Bgl II, Pst I, and Sph I RE fragments from NADC-1 was compared to those from the reference strain of PAV serotype 4 (F618), and to two recent isolates, NADC-2 and NADC-3. For all restriction enzymes examined, the sizes of the NADC-1 fragments were identical to PAV-4, NADC-2, and NADC-3 fragments, indicating that the NADC-1 isolate is very closely related, if not identical, to PAV-4 and two recent isolates. Southern blot hybridizations also indicated that NADC-1, NADC-2, NADC-3, and PAV-4 are very similar and revealed regions of sequence similarity between NADC-1 and human Ad-2 and human Ad-5.

Adenoviridae↗
PubMed1981

Comparison of the restriction endonuclease maps of unintegrated proviral DNAs from four xenotropic murine leukemia viruses.

From purified linear and superhelical DNAs, the restriction endonuclease maps of four xenotropic murine leukemia virus DNAs from NFS, NZB, BALB/c, and AKR mice were determined with ten restriction endonucleases. Each xenotropic proviral DNA was found to be a unique restriction endonuclease map, with differences in the gag, pol, env, and terminal repeated sequence regions. However, type-specific SacI and EcoRI sites in the env region were identical in all four xenotropic murine leukemia virus DNAs and were not found in ecotropic murine leukemia virus DNA. Comparison of the xenotropic murine leukemia virus DNA maps with maps of ecotropic murine leukemia virus DNA showed that the pol and terminal repeated sequence regions were highly conserved. Other similarities in ecotropic and some xenotropic viral DNAs suggest common origins.

Animals↗
PubMed1987

A large inverted duplication allows homologous recombination between chromosomes heterozygous for the proximal t complex inversion.

We have examined the molecular organization of a region of mouse chromosome 17 that allows homologous recombination between wild-type and t haplotype chromosomes across a large inversion. We have used a combination of genetic mapping of restriction fragment length polymorphisms, molecular characterization of cloned regions isolated on overlapping cosmids, and subchromosomal restriction mapping using the pulsed field gel technique. Our analyses show that the wild-type form of chromosome 17 contains an inverted duplication of an element of at least 650 kb that is present in only one copy in the t haplotype form. Two chromosomes, th45 and tAE5, arose by homologous recombination across the element that is present in both chromosomal variants in the same orientation.

Animals↗
PubMed1995

Polymorphism of genes coding for nuclear 18S rRNA indicates genetic distinctiveness of anastomosis group 10 from other groups in the Rhizoctonia solani species complex.

DNA polymorphism in the 18S nuclear rRNA gene region was investigated by using 11 restriction endonucleases for 161 isolates of 25 intraspecific groups (ISGs) representing 11 reported anastomosis groups (AGs) of Rhizoctonia solani. A PCR-based restriction mapping method in which enzymatically amplified DNA fragments and subfragments were digested with one or two restriction enzymes was employed. Four types of DNA restriction maps of this region were constructed for these 25 ISGs. Map type I of the 18S rDNA region was represented by isolates of a majority of R. solani ISGs. Map types II and III, represented by ISG 2E and 9 isolates and 5C isolates, respectively, differed from map I by the absence of one (map type II) or two (map type III) restriction sites. Map type IV, represented by ISG 10A and B (or AG 10) isolates, showed significant restriction site variations, with five enzymes in this region compared with those of the remaining ISGs or AGs. Ten of the 25 restriction sites in the 18S rRNA gene region were informative and selected for analysis. Previously reported restriction maps of the 5.8S rRNA gene region, including the internal transcribed spacers, were aligned with each other, and 12 informative restriction sites were identified. These data were used alone and in combination to evaluate group relationships. Analyses derived from these data sets by maximum parsimony and likelihood methods showed that AG 10 isolates were distinct and distantly related to the majority isolates of the other AGs of this species complex.

Base Sequence↗
PubMed1989

A program for storage and retrieval of demographic, sample, clinical laboratory, and restriction endonuclease map data.

A program, written in dBASE, is described that manages demographic, sample, clinical laboratory, and restriction endonuclease map data. The program exports migration distances of DNA fragments resulting from specified endonuclease digests to a commercially available, but modified, curve fitting program (CURVE-FITTER) where the fragment sizes in base pairs are calculated. The calculated values are imported back into dBASE files for report generation or later analysis. The program will produce hard copy reports for single or multiple individuals.

Clinical Laboratory Information Systems↗
PubMed1985

A restriction endonuclease map of Streptomyces phage VWB.

A physical map of the actinophage VWB has been constructed using the restriction endonucleases BglII, ClaI, EcoRI, EcoRV, HindIII, KpnI and SphI. Phage VWB, genome size 47.3 kb, propagates on Streptomyces venezuelae, and it can also lysogenise this species. The three BglII-generated fragments of VWB DNA were cloned in pBR322, and subsequently mapped. In this manner the restriction map of the VWB phage genome was constructed.

Bacteriophages↗
PubMed2003

Stretching of single DNA molecules by LB technique for restriction site mapping.

Stretched single DNA molecules were prepared on substrates by Langmuir-Blodgett (LB) method for the restriction site mapping. Stretched single Lambda DNA and EcoRI bound to the DNA were observed by scanning near-field optical microscope (SNOM). As a result, the specific binding sites of EcoRI on the Lambda DNA molecules were determined.

DNA↗
PubMed1983

Restriction endonuclease mapping of the root-inducing plasmid of Agrobacterium rhizogenes 1855.

The root-inducing plasmid of the agropine type Agrobacterium rhizogenes 1855 was mapped by means of the restriction endonuclease EcoRI. The circular arrangement of the more than 60 fragments generated by this enzyme was established by electrophoretic analysis of pBR322 clones harboring overlapping segments of pRi1855 derived by partial digestion with EcoRI. A large region of the plasmid comprising the T-DNA was mapped with two additional enzymes, BamHI and HindIII, by means of Southern blot hybridizations between the fragments generated by the three enzymes.

Chromosome Mapping↗
PubMed1988

FRAGMAP--a program for restriction site map comparison.

A program is described which aligns pairs of linear restriction site maps using an algorithm which maximizes the number of coincident sites through the addition of extra 'padding' fragments; and makes maps of the non-conserved sites between pairs and triplets of input maps. A range of display facilities, hardcopy functions and database management routines are also included. The program runs on a stand-alone microcomputer, and is stored along with a database of several hundred files on a single floppy disc.

Copying Processes↗
PubMed1994

[Specificity of the recombinant DNA pCX7 and its restriction enzyme map].

The recombinant DNA pCX7 derived from L. interrogans serovar lai strain 017 was applied for hybridization with 17 strains (8 serogroups of L. interrogans, L. biflexa strain Patoc I and Leptonema strain 3055); meanwhile 15 restriction endonucleases were used for analysis of the restriction enzyme map of pCX7. The result showed that the recombinant DNA probe is specific to species L. interrogans and its homology with DNA from different leptospires. A restriction enzyme map of pCX7 was constructed. Unique site for Bgl II and 3 sites for Bst BI were located within the cloned fragment (1.7 kb).

DNA, Bacterial↗
PubMed1982

Linkage arrangement of human placental lactogen and growth hormone genes.

Human placental lactogen (hPL) and growth hormone (hGH) are two hormones thought to have evolved from a common ancestral gene (along with prolactin), yet they have quite different functions and specificities. The nucleic acid sequences of the respective cDNAs of the two genes share considerable homology, as well as the existence of multiple forms of each gene within the genome. In this study we report on the linkage arrangement of several genes from this group. Two hPL-like genes as well as an hGH gene are shown to be linked within a 38-kilobase pair region of DNA. Linkage between a variant hGH gene and an hPL gene is also shown. The orientation and structural organization of these genes was previously established using 5'- and 3'-specific probes from a placental lactogen cDNA clone and detailed restriction endonuclease mapping. Restriction fragments from the overlapping clones were verified by comparison to digests of high molecular weight genomic DNA. In addition, the location of a specific class of repetitive DNA sequences, the Alu family, was mapped on these clones using the recombinant clone BLUR 8. All members of this multigene family have Alu repeat sequences either immediately flanking their 3' or 5' untranslated regions or within their intervening sequences.

Base Sequence↗
PubMed1984

Cloning and characterization of a Novikoff hepatoma ribosomal DNA-fragment containing the initiation site of transcription.

A 10.3 kilobase EcoRI fragment of Novikoff hepatoma rat ascites tumor ribosomal gene was cloned in pBR322 vector. The cloned fragment contained part of the 18S RNA gene, and about 8 kilobases of the 5' spacer region. A restriction map was constructed by cleavage of the fragment with BamHI, HindIII, KpnI, PstI, SstI and XhoI enzymes. A putative transcription initiation site for the 45S pre-ribosomal RNA was localized by P1 nuclease protection mapping at a distance of about 130 base pairs 5' to the HindIII site on the restriction map. Both the restriction map and the position of the initiation site of transcription were almost identical to those of the corresponding rat ribosomal DNA fragments.

Animals↗
PubMed1986

Naturally occurring TOL plasmids in Pseudomonas strains carry either two homologous or two nonhomologous catechol 2,3-oxygenase genes.

Structural genes for catechol 2,3-oxygenase (C23O) were cloned from the TOL plasmids pWW5, pWW14, pWW74, pWW84, and pWW88 isolated from Pseudomonas strains of diverse geographical origins. Each pKT230-based C23O+ recombinant plasmid carried a 2.05-kilobase XhoI insert which showed strong homology in Southern hybridizations with the xylE gene from the archetype TOL plasmid pWW0. Fragments were mapped for restriction endonuclease sites and were classified into two closely related groups on the basis of restriction maps. C23O structural genes were located on cloned fragments by a combination of subcloning and site-specific mutagenesis. All five TOL plasmids examined yielded clones whose maps differed from that of xylE of pWW0 by only a single XbaI site, but in addition plasmids pWW5, pWW74, and pWW88 carried a second, homologous C23O gene with seven further restriction site differences. The remaining plasmids, pWW14 and pWW84, carried a second nonhomologous C23O gene related to the second C23O gene (C23OII) of TOL plasmid pWW15 described previously (H. Keil, M. R. Lebens, and P. A. Williams, J. Bacteriol. 163:248-255, 1985). Thus, each naturally occurring TOL plasmid in this study appears to carry genes for two meta cleavage dioxygenases.

Catechol 2,3-Dioxygenase↗