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Proceedings of the National Academy of... Oct 2006The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes;...
The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are "in the noise" or "slightly above the noise." We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.
Topics: Algorithms; DNA; Escherichia coli; Humans; Restriction Mapping
PubMed: 17043225
DOI: 10.1073/pnas.0604040103 -
Veterinary Microbiology Jun 2005Our current knowledge of antigenic variability of the bovine respiratory syncytial virus (BRSV) is quite limited and is mainly dependent on the use of monoclonal...
Our current knowledge of antigenic variability of the bovine respiratory syncytial virus (BRSV) is quite limited and is mainly dependent on the use of monoclonal antibodies (mAb). In this study, we present not only analysis of the antigenic, but also of the genetic variability of BRSV. Using a panel of BRSV-specific mAb we distinguished five main reactivity patterns, three of which corresponded to the previously established subgroups A, B and AB. A single viral strain yielded the fourth pattern, while four viral strains did not react with any of the used mAbs forming the fifth pattern. To investigate the genetic basis for the antigenic heterogeneity of the BRS virus G protein, DNA of 11 BRSV isolates was directly sequenced. The comparison of the obtained nucleotide or amino acid sequences to those BRSV strains present in the GenBank revealed 88.1-99.4% and 77.7-98.4% similarity, respectively. These results supported the previously stated suggestion to type BRSV isolates according to their genetic relationship. In order to introduce a rapid and simple method to study the genetic variability of BRSV, we utilized the restriction enzyme analysis of RT-PCR products derived from mRNAs corresponding to the most variable region of the BRSV glycoprotein G ectodomain. Using this restriction enzyme analysis we were able to identify genetic variability among BRSV isolates. The detected non-synonymous mutations led frequently to a change in digestion pattern and were predominantly located in two mucin-like regions of the G protein gene. A correlation has been found between grouping of isolates in the phylogenetic tree and their restriction patterns clustering together isolates with the same restriction profiles. However, viruses placed distant in the tree sharing the same restriction patterns were detected supposing that phylogenetic analysis should be necessary for BRSV typing. Thus, we propose to use DNA restriction polymorphism for a rapid detection of genetic variants among BRSV isolates circulating in cattle population and as a preliminary tool for their typing.
Topics: Amino Acid Sequence; Antibodies, Monoclonal; Antibodies, Viral; Antigens, Viral; Genetic Variation; Molecular Sequence Data; Phylogeny; Respiratory Syncytial Virus, Bovine; Restriction Mapping; Reverse Transcriptase Polymerase Chain Reaction; Sequence Alignment; Sequence Homology, Amino Acid; Viral Proteins
PubMed: 15917131
DOI: 10.1016/j.vetmic.2005.02.008 -
Genes Apr 2019The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, , is an economically important...
The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, , is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick and wide calipash, and lower body fat. In this study, ten male and ten female turtles were subjected to restriction site-associated DNA sequencing (RAD-seq) using the Hi-Seq 4000 sequencing platform to isolate female-specific DNA fragments. We identified 5967 bp and 6532 bp fragments using genome walking. Three female-specific markers designed from these two fragments were confirmed to separate the sexes of perfectly. One of the female-specific markers showed dosage association in female and male individuals. Individuals from different populations (n = 296) were used to validate that the female-specific markers could identify the genetic sex of with 100% accuracy. The results of the present study demonstrated that RAD-seq was useful to develop sex-related markers in animals, and verified that the sex determination system of belonged to the ZZ/ZW heterogametic system. Importantly, the developed markers could lead to a method for sex-controlled breeding in the Chinese soft-shelled turtle.
Topics: Animals; Body Size; Female; Gene Dosage; Genetic Markers; Genome-Wide Association Study; Male; Restriction Mapping; Sequence Analysis, DNA; Sex Characteristics; Turtles
PubMed: 30991756
DOI: 10.3390/genes10040302 -
Journal of Computational Biology : a... 1998Consider a mapping project in which overlap of clonal segments is inferred from complete multiple restriction digests. The fragment sizes of the clones are measured with...
Consider a mapping project in which overlap of clonal segments is inferred from complete multiple restriction digests. The fragment sizes of the clones are measured with some error, potentially leading to a map with erroneous links. The number of errors in the map depends on the number and types of enzymes used to characterize the clones. The most critical parameter is the decision rule k, or the criterion for declaring clone overlap. Small changes in k may cause an order of magnitude change in the amount of work it takes to build a map of given completion. We observe that the cost of an optimal mapping strategy is approximately proportional to the target size. While this finding is encouraging, considerable effort is nonetheless required: for large-scale sequencing projects with up-front mapping, mapping will be a non-negligible fraction of the total sequencing cost.
Topics: Chromosome Mapping; DNA; DNA Restriction Enzymes; Poisson Distribution; Restriction Mapping; Sequence Analysis, DNA
PubMed: 9541875
DOI: 10.1089/cmb.1998.5.113 -
Cold Spring Harbor Protocols Dec 2019The easiest way to confirm the structure and identity of genomic DNA isolated from purified adenoviral recombinants is restriction enzyme digestion and gel...
The easiest way to confirm the structure and identity of genomic DNA isolated from purified adenoviral recombinants is restriction enzyme digestion and gel electrophoresis. This analysis entails comparing the restriction patterns of the adenoviral vector DNA with that plasmid that was used to initiate the entire rescue and expansion process. The integrity of the viral backbone and the presence of both the transgene and viral ITRs are assessed.
Topics: Adenoviridae; DNA, Viral; Genetic Vectors; Genome, Viral; Recombination, Genetic; Restriction Mapping
PubMed: 31792137
DOI: 10.1101/pdb.prot095554 -
Artificial Intelligence in Medicine Oct 1993Restriction mapping is an important computational problem in molecular biology, particularly in genetic engineering and DNA sequencing. It is different in that it is not...
Restriction mapping is an important computational problem in molecular biology, particularly in genetic engineering and DNA sequencing. It is different in that it is not only a purely computational problem but involves an interaction between experimental data collection procedures and the mapping algorithms. Consequently, the problem is loosely defined and in practice requires a flexible and versatile algorithm. We describe a framework for solving many restriction mapping problems in the constraint logic programming language CLP (R) which takes advantage of the declarative and powerful features of constraint logic programming. A CLP (R) algorithm is developed for solving a simple restriction mapping problem. The algorithm is the extended to handle more complex variations of restriction mapping such as fragments with errors, circular maps, multiple enzymes and partial digests. The mapping variants are integrated within the same framework and differ in the constraints required to define the kind of map consistency. Various search heuristics and control strategies to improve the search process are also incorporated as constraints.
Topics: Algorithms; Electrophoresis, Polyacrylamide Gel; Enzymes; Hydrolysis; Logic; Restriction Mapping; Sequence Analysis, DNA; Software
PubMed: 8004144
DOI: 10.1016/0933-3657(93)90036-3 -
Computer Applications in the... Jul 1990This paper presents an algorithm that searches a DNA restriction enzyme map for regions that approximately match a shorter 'probe' map. Both the map and the probe...
This paper presents an algorithm that searches a DNA restriction enzyme map for regions that approximately match a shorter 'probe' map. Both the map and the probe consist of a sequence of address-enzyme pairs denoting restriction sites, and the algorithm penalizes a potential match for undetected or missing sites and for discrepancies in the distance between adjacent sites. The algorithm was designed specifically for comparing relatively short DNA sequences with a long restriction map, a problem that will become increasing common as large physical maps are generated. The algorithm has been used to extract information from a restriction map of the entire Escherichia coli genome.
Topics: Algorithms; Restriction Mapping; User-Computer Interface
PubMed: 2207749
DOI: 10.1093/bioinformatics/6.3.247 -
Biochemical Genetics Dec 2018Chinese wolfberry (Lycium spp.) is an important edible and medicinal plant, with a long cultivation history. The genetic relationships among wild Lycium species and...
Chinese wolfberry (Lycium spp.) is an important edible and medicinal plant, with a long cultivation history. The genetic relationships among wild Lycium species and landraces have been unclear for a number of reasons, which has hindered the breeding of modern Chinese wolfberry cultivars. In this study, we collected 19 accessions of Chinese wolfberry germplasm, and constructed the genetic relationship based on RAD-seq markers. We obtained 30.32 Gb of clean data, with the average value of each sample being 1.596 Gb. The average mapping rate was 85.7%, and the average coverage depth was 6.76 X. The phylogeny results distinguished all accessions clearly. All the studied landraces shared their most recent common ancestor with L. barbarum, which indicated that L. barbarum may be involved in cultivation of these landraces. The relationship of some landraces, namely the 'Ningqi' series, 'Qingqi-1' and 'Mengqi-1,' has been supported by the phylogeny results, while the triploid wolfberry was shown to be based on a hybrid between 'Ningqi-1' and a tetraploid wolfberry. This study uncovered the genetic background of Chinese wolfberry, and developed the foundation for species classification, accession identification and protection, and the production of hybrid cultivars of wolfberry.
Topics: Chromosomes, Plant; Genes, Plant; Genetic Markers; High-Throughput Nucleotide Sequencing; Lycium; Phylogeny; Restriction Mapping
PubMed: 29876687
DOI: 10.1007/s10528-018-9861-x -
Journal of Computational Biology : a... 1999Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many...
Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many potential applications in DNA sequencing and genetics. In this work, we present a heuristic algorithm for fragment identification, a key step in the process of constructing an MCD map. Given measurements of the restriction fragment sizes from one or more complete digestions of each clone in a clone library covering the molecule to be mapped, the algorithm identifies groups of restriction fragments on different clones that correspond to the same region of the target DNA. Once these groups are correctly determined the desired map can be constructed by solving a system of simple linear inequalities. We demonstrate the effectiveness of our algorithm on real data provided by the Genome Center at the University of Washington.
Topics: Algorithms; Chromosomes, Artificial, Yeast; Chromosomes, Human, Pair 6; Computational Biology; Contig Mapping; Cosmids; DNA Restriction Enzymes; DNA, Recombinant; Gene Library; Genome, Human; Humans; Logic; Molecular Weight; Reproducibility of Results; Restriction Mapping; Software; Washington
PubMed: 10421522
DOI: 10.1089/cmb.1999.6.187 -
Oral Microbiology and Immunology Apr 1993The size, configuration and restriction map of Actinobacillus actinomycetemcomitans bacteriophage phi Aa DNA was determined by means of restriction endonuclease...
The size, configuration and restriction map of Actinobacillus actinomycetemcomitans bacteriophage phi Aa DNA was determined by means of restriction endonuclease analysis. Digestion of the phi Aa DNA with restriction enzymes Hind III, Eco RI and Sal I produced 6, 5, and 4 fragments, respectively. Based upon the sum of the sizes of the restriction fragments of these enzymes, the DNA was estimated to be 47.2 kilobase pairs in length. A restriction map was constructed using Hind III and Sal I. Incubation with exonuclease Bal 31 for increasing lengths of time resulted in progressive hydrolysis of the DNA, as expected for a linear molecule. No sub-molar fragments or diffuse bands were observed in the agarose gels of the restriction endonuclease digests of the phi Aa DNA. Attempts at ligating the ends of the DNA were consistently unsuccessful. Therefore, we found no evidence for cohesive ends, a circular permutation of the genome or for headful packaging mechanism from a concatameric DNA precursor.
Topics: Aggregatibacter actinomycetemcomitans; Bacteriophages; DNA, Viral; Genome, Viral; Restriction Mapping
PubMed: 8355982
DOI: 10.1111/j.1399-302x.1993.tb00553.x