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Journal of Microbiological Methods May 2007REMA is an interactive web-based program which predicts endonuclease cut sites in DNA sequences. It analyses multiple sequences simultaneously and predicts the number...
UNLABELLED
REMA is an interactive web-based program which predicts endonuclease cut sites in DNA sequences. It analyses multiple sequences simultaneously and predicts the number and size of fragments as well as provides restriction maps. The users can select single or paired combinations of all commercially available enzymes. Additionally, REMA permits prediction of multiple sequence terminal fragment sizes and suggests suitable restriction enzymes for maximally discriminatory results. REMA is an easy to use, web based program which will have a wide application in molecular biology research.
AVAILABILITY
REMA is written in Perl and is freely available for non-commercial use. Detailed information on installation can be obtained from Jan Szubert ([email protected]) and the web based application is accessible on the internet at the URL http://www.macaulay.ac.uk/rema
CONTACT
Topics: DNA Restriction Enzymes; DNA, Bacterial; Restriction Mapping; Software
PubMed: 17346831
DOI: 10.1016/j.mimet.2007.01.008 -
Journal of Computational Biology : a... 1997In this paper, we describe our algorithmic approach to constructing ordered restriction maps based on the data created from the images of population of individual DNA...
In this paper, we describe our algorithmic approach to constructing ordered restriction maps based on the data created from the images of population of individual DNA molecules (clones) digested by restriction enzymes. The goal is to devise map-making algorithms capable of producing high-resolution, high-accuracy maps rapidly and in a scalable manner. The resulting software is a key component of our optical mapping automation tools and has been used routinely to map cosmid, lambda and BAC clones. The experimental results appear highly promising.
Topics: Algorithms; Bacteriophage lambda; Bayes Theorem; Chromosomes, Bacterial; Cosmids; Humans; Models, Genetic; Models, Statistical; Restriction Mapping
PubMed: 9228610
DOI: 10.1089/cmb.1997.4.91 -
Methods in Molecular Biology (Clifton,... 1997
Topics: Restriction Mapping; Sequence Analysis, DNA; Software
PubMed: 9089618
DOI: No ID Found -
Analytical Biochemistry Feb 1997
Topics: Cosmids; Electrophoresis, Agar Gel; Endodeoxyribonucleases; Genetic Markers; Restriction Mapping
PubMed: 9025976
DOI: 10.1006/abio.1996.9956 -
PloS One 2018The P8 stem-loop region of the trnL intron, which is known to be hypervariable in size with multiple repeat motifs and created difficulties in alignment, is always...
The P8 stem-loop region of the trnL intron, which is known to be hypervariable in size with multiple repeat motifs and created difficulties in alignment, is always excluded in phylogenetic as well as barcode analyses. This region was investigated for species discrimination in 98 taxa of orchids belonging to the tribe Vandeae using in silico mapping of restriction site polymorphism. The length of the P8 regions varied from 200 nucleotides in Aerides rosea to 669 nucleotides in Dendrophylax sallei. Forty two taxa had unique lengths, while as many as eight shared a common length of 521 nucleotides. Of the 35 restriction endonucleases producing digestions in the P8 regions, three, viz., AgsI, ApoI and TspDTI turned out to have recognition sites across all the 98 taxa being studied. When their restriction data were combined, 92 taxa could be discriminated leaving three taxon pairs. However, Acampe papillosa and Aeranthes arachnites despite having similar restriction sites differed in their P8 lengths. This is the first report on thorough investigation of the P8 region of trnL intron for search of species specific restriction sites and hence its use as a potential plant DNA barcode.
Topics: Genome, Plant; Introns; Orchidaceae; Phylogeny; Polymorphism, Genetic; Restriction Mapping; Sequence Alignment
PubMed: 29718976
DOI: 10.1371/journal.pone.0196680 -
Bioinformatics (Oxford, England) Aug 2019Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the...
SUMMARY
Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research.
AVAILABILITY AND IMPLEMENTATION
MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM).
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Chromosome Mapping; Genomics; Restriction Mapping; Sequence Analysis, DNA; Software
PubMed: 30535283
DOI: 10.1093/bioinformatics/bty1013 -
Nucleic Acids Research Nov 1989
Topics: Bacteriophage lambda; DNA Transposable Elements; Genetic Vectors; Restriction Mapping
PubMed: 2555794
DOI: 10.1093/nar/17.22.9494 -
Proceedings. International Conference... 1994Restriction mapping generally requires the application of information from various digestions by restriction enzymes to find solution sets. We use both the predicate...
Restriction mapping generally requires the application of information from various digestions by restriction enzymes to find solution sets. We use both the predicate calculus and constraint solving capabilities of CLP(R) to develop an engine for restriction mapping. Many of the techniques employed by biologists to manually find solutions are supported by the engine in a consistent manner. We provide generalized pipeline and cross-multiply operators for combining sub-maps. Our approach encourages the building of maps iteratively. We show how other techniques can be readily incorporated.
Topics: Animals; Computer Simulation; DNA; Humans; Restriction Mapping; Software
PubMed: 7584380
DOI: No ID Found -
BMC Bioinformatics Aug 2018Restriction enzymes are used frequently in biotechnology. However, manual mining of restriction enzymes is challenging. Furthermore, integrating available restriction...
BACKGROUND
Restriction enzymes are used frequently in biotechnology. However, manual mining of restriction enzymes is challenging. Furthermore, integrating available restriction enzymes into different bioinformatics systems is necessary for many biotechnological applications, such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Thus, in the present study, we developed the package REHUNT (Restriction Enzymes HUNTing), which mines restriction enzymes from the public database REBASE using a series of search operations.
RESULTS
REHUNT is a reliable and open source package implemented in JAVA. It provides useful methods and manipulations for biological sequence analysis centered around restriction enzymes contained in REBASE. All available restriction enzymes for the imported biological sequences can be identified by REHUNT. Different genotypes can be identified using PCR-RFLP based on REHUNT for single nucleotide polymorphism (SNP), mutations, and the other variations. REHUNT robustly recognizes multiple inputs with different formats, e.g. regular DNA sequences, variation-in-sequence indicated by IUPAC code, as well as variation-in-sequence indicated by dNTPs format. Variations including di-, tri-, and tetra-allelic types and indel formats are also acceptable. Furthermore, REHUNT provides classified restriction enzymes output, including IUPAC and general sequence types, as well as commercial and non-commercial availabilities. REHUNT also enables analysis for high throughput screening (HTS) technologies.
CONCLUSIONS
REHUNT is open source software with GPL v3 license and can be run on all platforms. Its features include: 1) Quick restriction enzymes search throughout a sequence based on the Boyer-Moore algorithm; 2) all available restriction enzymes provided and regularly updated from REBASE; 3) an open source API available of integrating all types of bioinformatics systems and applications; 4) SNP genotyping available for plant and animal marker-assisted breeding, and for human genetics; and 5) high throughput analysis available for Next Generation Sequencing (NGS). REHUNT not only to effectively looks for restriction enzymes in a sequence, but also available for SNP genotyping. Furthermore, it can be integrated into other biological and medical applications. REHUNT offers a convenient and flexible package for powerful restriction enzymes analyses in association studies, and supports high throughput analysis. The source codes and complete API documents are available at SourceForge: https://sourceforge.net/projects/rehunt/ , GitHub: https://github.com/yuhuei/rehunt , and at: https://sites.google.com/site/yhcheng1981/rehunt .
Topics: DNA Restriction Enzymes; Humans; Restriction Mapping; Software
PubMed: 30092755
DOI: 10.1186/s12859-018-2168-4 -
Molecular Biotechnology Jul 2001With the explosion in genetic information and almost complete sequencing of the human genome, a shift in the experimental goals of molecular biologists is occurring.... (Review)
Review
With the explosion in genetic information and almost complete sequencing of the human genome, a shift in the experimental goals of molecular biologists is occurring. Instead of focusing on single genes, current attempts seek to divine the interactions of several genes and sequences. This requires increasingly complex genetic constructs and manipulations, often of very large DNA constructs, and these can be made with RecA protein-based techniques. When RecA protein combined with an oligonucleotide acts as a sequence-specific "masking tape" to block DNA from the action of DNA modifying enzymes, and can be used to direct the cleavage of DNA at single predetermined restriction endonuclease sites. This reaction is called RecA-Assisted Restriction Endonuclease (RARE) Cleavage. The reverse reaction, known as RecA-Assisted Ligation, can be used to join any two desired fragments. When one of those fragments is a vector, a desired fragment can be cloned directly without constructing a genomic library. The reagents and equipment needed are relatively inexpensive, and almost any desired genetic construct up to about 300 kb in size can be made in a straightforward manner.
Topics: Animals; DNA, Neoplasm; Genetic Engineering; Humans; Rec A Recombinases; Restriction Mapping
PubMed: 11503517
DOI: 10.1385/MB:18:3:233