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PubMed1984

KLONER; a computer program to simulate recombinant DNA strategies by restriction map manipulation.

A computer program is described which allows for the manipulation of restriction maps of various DNA fragments to demonstrate techniques used in DNA cloning and to predict and/or confirm experimental results. This program is capable of reading in restriction enzyme cleavage sites for several different DNA molecules of interest. This information is then compiled in order to form restriction maps which can then be processed by digestion with restriction endonucleases and treatment with other common DNA modifying enzymes. Ligation can then be simulated by joining fragments with complementary ends in all possible orientations, producing restriction maps of the products. The resulting recombinants can then be further analyzed by physical mapping with appropriate restriction endonucleases. This program was written in Pascal on an Apple II computer.

Base Sequence↗
PubMed1991

Partial restriction map of salmonid herpesvirus (Oncorhynchus masou virus) DNA for three restriction enzymes BamHI, EcoRI and XhoI.

Cleavage of Oncorhynchus masou virus (OMV) DNA with restriction endonucleases BamHI, EcoRI, and XhoI resulted in 28, 26 and 17 fragments, respectively. Based on the molecular weights of digested fragments and those molar ratio. OMV DNA showed the molecular weight of about 100 x 10(6). Twenty out of 28 BamHI fragments of OMV DNA were successfully cloned into pBR322 vector. Restriction map of OMV DNA was constructed by blotting hybridization and double-digestion. The data suggested that terminal repeat of the end fragments of OMV DNA molecule was not existence.

Animals↗
PubMed1986

A computer program package for restriction map analysis and manipulation.

Programs for the calculation, storage and analysis of restriction maps derived from the analysis of partial digestion products from end labelled DNA (1,2,3) and their correlation with digestion - and hybridisation patterns in total digestions and Southern blot experiments are described. These programs allow direct input of gel patterns from partial or complete digestion experiments using a digitizer tablet, calculation of molecular weights and restriction maps, plotting of maps and actual or predicted fragment patterns and automated identification of overlapping cosmids from partial restriction mapping results. Programs are written in PASCAL and have been implemented on a VAX/VMS system, with a HP-7221T plotter and a digitizing tablet.

Cloning, Molecular↗
PubMed1992

Dynamic programming algorithms for restriction map comparison.

For most sequence comparison problems there is a corresponding map comparison algorithm. While map data may appear to be incompatible with dynamic programming, we show in this paper that the rigor and efficiency of dynamic programming algorithms carry over to the map comparison algorithms. We present algorithms for restriction map comparison that deal with two types of map errors: (i) closely spaced sites for different enzymes can be ordered incorrectly, and (ii) closely spaced sites for the same enzyme can be mapped as a single site. The new algorithms are a natural extension of a previous map comparison model. Dynamic programming algorithms for computing optimal global and local alignments under the new model are described. The new algorithms take about the same order of time as previous map comparison algorithms. Programs implementing some of the new algorithms are used to find similar regions within the Escherichia coli restriction map of Kohara et al.

Algorithms↗
PubMed1988

Construction of restriction maps.

A computer program is described, which constructs maps of restriction endonuclease cleavage sites in linear or circular DNA molecules, given the fragment lengths in single and double digestions with two enzymes. The algorithm is based upon a partition method and a very simple rule to chain fragments. The program is written in Prolog II.

Algorithms↗
PubMed1984

PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic display of conventional restriction maps.

We describe an interactive computational tool, PLASMAP, which allows the user to electronically store, retrieve, and display circular restriction maps. PLASMAP permits users to construct libraries of plasmid restriction maps as a set of files which may be edited in the laboratory at any time. The display feature of PLASMAP quickly generates device-independent, artist-quality, full-color or monochrome, hard copies or CRT screens of complex, conventional circular restriction maps.

Base Sequence↗
PubMed1985

Novel approach for restriction mapping repetitive DNA elements using DNA transformation.

We demonstrated that DNA transformation can be used to determine the linkage relationship between DNA restriction fragments in mouse genomic DNA. Using this experimental approach, we obtained linkage information which enabled us to construct a restriction map for the multiple thymidine kinase (tk) gene inserts present in a mouse L-cell line. This restriction map included cutting sites for seven restriction enzymes spanning a distance of over 10 kb. It revealed that the tk inserts in this cell line are arranged in a complex array consisting of direct and inverted repeats. In light of these results, we suggest that this approach will be particularly useful for restriction mapping DNA sequences that are repetitive as such DNA may be difficult to characterize by conventional methods alone.

Animals↗
PubMed1998

Mapper: an intelligent restriction mapping tool.

MOTIVATION: To determine the most powerful artificial intelligence techniques for automated restriction mapping, and use them to create a powerful multiple-enzyme restriction mapping tool. RESULTS: The most effective search engine utilized model-driven exhaustive search and a form of binary logic pruning based on Pratt's separation theory. Additional experimentation led to the development of an input preprocessing module which significantly speeds up searches, and an output post-processing module which enables users to analyze large solution sets and reduce their apparent complexity. AVAILABILITY: An executable version of the resultant tool, Mapper, can be downloaded from our Web site (http://www.ai.eecs.uic.edu) by selecting the 'Software' option. CONTACT: nelson@eecs.uic.edu (http://www.ai.eecs.uic.edu/ñelson).

Algorithms↗
PubMed1985

Computer-aided construction of nucleic acid restriction maps using defined vectors.

A new algorithm is described that will rapidly produce restriction maps of cloned DNA fragments. Information concerning the vector is stored as a data file and used in constructing probable maps. As the program is based upon a permutation analysis it has two primary uses. First, preliminary restriction maps can be created from fragment length data as a starting point for further analysis. Second, existing maps can be confirmed as being highly probable, and other probable maps examined to ensure certain combinations have not been overlooked. Although primarily designed for linear vectors, the program can be used to calculate circular maps.

Algorithms↗
PubMed1998

A uniform framework for ordered restriction map problems.

Optical Mapping is an emerging technology for constructing ordered restriction maps of DNA molecules. The underlying computational problems for this technology have been studied and several models have been proposed in recent literature. Most of these propose combinatorial models; some of them also present statistical approaches. However, it is not a priori clear as to how these models relate to one another and to the underlying problem. We present a uniform framework for the restriction map problems where each of these various models is a specific instance of the basic framework. We achieve this by identifying two "signature" functions f() and g() that characterize the models. We identify the constraints these two functions must satisfy, thus opening up the possibility of exploring other plausible models. We show that for all of the combinatorial models proposed in literature, the signature functions are semi-algebraic. We also analyze a proposed statistical method in this framework and show that the signature functions are transcendental for this model. We also believe that this framework would provide useful guidelines for dealing with other inferencing problems arising in practice. Finally, we indicate the open problems by including a survey of the best known results for these problems.

Algorithms↗
PubMed1981

Cloning and restriction mapping of the alkaline phosphatase structural gene (phoA) of Escherichia coli and generation of deletion mutants in vitro.

The structural gene for alkaline phosphatase (phoA) of Escherichia coli was cloned into the PstI site of pBR322, from a transducing bacteriophage, lambda p(phoA-proC). The restriction map of the plasmid was established. Based upon this information, several phoA deletion plasmids as well as a smaller phoA+ plasmid were constructed. The genetic map and restriction map were correlated by recombination analysis. Cells carrying one of the phoA+ plasmids overproduce alkaline phosphatase 10-fold upon phosphate limitation. However, both regulation and processing of the enzyme were found to be normal.

Alkaline Phosphatase↗
PubMed1995

An anchored restriction-mapping approach applied to the genetic analysis of the Anopheles gambiae malaria vector complex 1.

We introduce here a simple approach for rapidly determining restriction maps for a number of regions of a genome; this involves "anchoring" a map with a rare restriction site (in this case the seldom-cutting EagI) followed by partial digestion of a frequent-cutting enzyme (e.g., Sau 3A). We applied this technology to five species of the Anopheles gambiae complex. In a single Southern blot we obtained about a 15-kb restriction map each for the mtDNA, rRNA gene, and a scnDNA region for each of five species. Phylogenetic analyses of these regions yield trees at odds with the more traditional chromosome inversion-based trees. The value of the approach for systematic purposes is the ease with which several large, independent regions of the genome can be quickly assayed for molecular variation.

Animals↗
PubMed1986

Rates of nuclear DNA evolution in pheasant-like birds: evidence from restriction maps.

To examine the tempo of genomic evolution in birds, we mapped 161 restriction sites in the nuclear DNA of seven species of birds belonging to the pheasant superfamily Phasianoidea. The three regions mapped lie on different chromosomes and bear eight genes, coding for lysozyme c, three "alpha-like" globins, and four "beta-like" globins. Together, the three regions span about 56 kilobases, most of which is presumably noncoding. The maps differed from one another at a minimum of 77 sites and by 9 length mutations. The extent of sequence divergence due to base substitutions was inferred to be similar for all three regions, even though the three coding regions differ by 5-fold from one another in mean rate of evolution at the amino acid level. A tree relating the maps differs in branching order from that implied by the traditional classification of phasianoid birds and is supported by published protein comparisons. Five of the nodes in the tree were associated with fossil evidence and historical biogeographic information, allowing us to estimate the mean rate of DNA divergence to be 0.34-0.40% per million years. This rate is similar to that estimated for the globin gene regions of higher primates, which validates the concept of an evolutionary clock at the DNA level. Our fossil-based calibration of DNA evolution differs by a factor of almost 2 from that proposed by others on the basis of biogeography. In consequence, published estimates of divergence times for birds and primates that are based on a biogeographically calibrated DNA clock may be too long.

Animals↗
PubMed1997

Construction of two near-kilobase resolution restriction maps of the 5' regulatory region of the human apolipoprotein B gene by quantitative DNA fiber mapping (QDFM).

Quantitative DNA fiber mapping (QDFM) is a high-resolution technique for physical mapping of DNA. The method is based on hybridization of fluorescently labeled DNA probes to individual DNA molecules stretched on a chemically modified glass surface. We now demonstrate and validate a rapid QDFM-based approach for the mapping of multiple restriction sites and precise localization of restriction fragments in large genomic clones. Restriction fragments of a 70-kb P1 clone (P1-70) containing the 5' region of the human apolipo-protein B gene (APOB) were subcloned and mapped along straightened P1-70 DNA molecules. Multicolor fluorescence in situ hybridization (FISH) and digital image analysis allowed us to rapidly position 29 restriction fragments, ranging in size from 0.5 kb to 8 kb, and to map 43 restriction sites. The restriction map obtained by QDFM was in excellent agreement with information obtained by RecA-assisted restriction endonuclease (RARE) cleavage, long-range PCR, and DNA sequence analyses of the P1-70 clone. These data demonstrate that QDFM is a rapid, reliable method for detailed restriction site-mapping of large DNA clones.

Apolipoproteins B↗
PubMed1991

Refinement of human chromosome 7 map around the pro alpha 2(I)collagen gene by long-range restriction mapping.

The physical proximity of the closely linked pro alpha 2(1)collagen (COL1A2) and erythropoietin (EPO) genes and five loci with no known function was studied by long-range restriction mapping experiments using pulsed-field gel electrophoresis. COL1A2 and D7S64 were found to be within 100 kb of each other, providing a new informative marker for linkage studies with respect to COL1A2. D7S15 and D7S79 were within 350 kb of each other. The physical distance between COL1A2 and EPO was determined to be at least 600 kb. Two CpG rich islands were recognized within 600 kb of COL1A2, suggesting that other genes might lie in the vicinity of COL1A2.

Chromosomes, Human, Pair 7↗
PubMed1988

Restriction map construction using a 'complete sentences compatibility' algorithm.

We have developed a new algorithm 'Complete sentences compatibility' (CSC) which uses single and double digestion fragments to rapidly determine restriction maps of circular DNA. From possible combinations of fragments of each simple digestion, which we call 'sentences of decomposition', we construct a restriction map which combines the sentences while taking into account compatibility rules. The algorithm can also deal with experimental errors of fragment weight and can suggest solutions that account for non-readable bands (fragments of zero length or multiple bands) on the gel. Because experiments using pairs of restrictive enzymes often result in multiple solutions, a complementary algorithm tries to reduce the number of proposed solutions by establishing consensus maps. The restriction map construction algorithm was tested on real cases, some containing more than fifteen fragments. Execution times range from 1-10 s on an IBM PC compatible microcomputer.

Algorithms↗
PubMed1988

New cloning vectors and techniques for easy and rapid restriction mapping.

We have modified plasmid, phage lambda and cosmid cloning vectors to be of general use for easily and unambiguously determining restriction maps of recombinant DNA molecules. Each vector is constructed so that it contains the rarely found NotI restriction site joined to a short synthetic linker sequence that is followed by a multiple cloning site. DNA cloned into these vectors may be restriction-mapped by either of two methods. In one technique, the cloned DNA is completely digested with NotI, followed by partial digestion with any other restriction enzyme. After electrophoresis and transfer to a nylon membrane, the fragments are hybridized to a labeled probe complementary to the NotI linker. In the second technique, referred to as recession hybridization detection, cloned DNA is digested with NotI and then briefly treated with exonuclease III to recess the 3' ends. After hybridizing a labeled complementary oligodeoxynucleotide to the single-stranded 5' end containing the linker sequence, the DNA is partially digested with another restriction enzyme, electrophoresed and the gel is exposed to x-ray film. With either method the size of each labeled fragment corresponds directly to the distance that a restriction site is located from the NotI linker terminus. Methods for obtaining partial restriction enzyme digests have been devised so that as many as 20 different enzymes may be conveniently mapped on a single gel in little more than a day. The vectors and techniques described may also be adapted to automated or semi-automated devices that read fragment lengths and calculate the resulting restriction map.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophage lambda↗
PubMed1991

Tn5cos: a transposon for restriction mapping of large plasmids using phage lambda terminase.

A method for the rapid restriction mapping of large plasmids has been developed. A 400-bp fragment of phage lambda DNA containing the cos region has been inserted into Tn5. After in vivo transposition of this Tn5cos element into the plasmid of choice, the plasmid is isolated and linearized at its cos site with phage lambda terminase (Ter). Such Ter linearization was about 70% efficient. After partial digestion of the linear molecules with the appropriate restriction enzyme, the products are selectively labelled at the right or left cohesive phage lambda DNA termini by hybridization with digoxygenin (DIG)-11-dUTP-labelled (using terminal transferase) oligodeoxyribonucleotides complementary to the single-stranded cos ends. After pulsed field gel electrophoresis, the labelled fragments are visualized in the dried gel using a DIG-detection kit. The restriction map can be directly determined from the 'ladder' of partial digestion products.

DNA Transposable Elements↗