36 results about "Restriction map" patented technology

A method and system are provided for comparing ordered segments of a first DNA restriction map with ordered segments of a second DNA restriction map to determine a level of accuracy the first DNA map and / or the second DNA map. In particular, the first and second DNA maps can be received (the first DNA map corresponding to a sequence DNA map, and the second DNA map corresponding to a genomic consensus DNA map as provided in an optical DNA map). Then, the accuracy of the first DNA map and / or the second DNA map is validated based on information associated with the first and second DNA maps. In addition, a method and system are provided for aligning a plurality of DNA sequences with a ordered DNA restriction map. The DNA sequences and the DNA map are received (the DNA sequences being fragments of a genome and the DNA map corresponding to a genomic consensus DNA map which relates to an optical ordered DNA map). Then, a level of accuracy of the DNA sequences and the DNA map is obtained based on information associated with the DNA sequences and the DNA map by means of the method and system described above. The locations of the DNA map at which the DNA sequences are capable of being associated with particular segments of the DNA map are located. Furthermore, it is possible to obtain locations of the DNA map (without the validation) by locating an optimal one of the locations for each of the DNA sequences for each of the locations.

Methods, computer-accessible medium, and systems for generating a genome wide probe map and / or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.

Disclosed is a computer-implemented method of determining at least one optimal alignment of at least part of a first map to at least part of a second map or a plurality of second maps, wherein the maps are physical genome maps and / or restriction maps. The method comprises: receiving first map data indicative of a first ordered list of distances between features of the first map, receiving second map data indicative of a second ordered list of distances between features of the second map or second maps; generating, from the second map data, seed data indicative of a plurality of seeds, each seed comprising at least one of the distances in the second ordered list, wherein the features are restriction sites and distances are fragment sizes. The said method further comprises generating a plurality of candidate alignments from the seed data by searching at least part of the first ordered list to find at least approximate matches for respective seeds, and extending the approximate matches bydynamic programming; determining respective alignment scores for respective candidate alignments; and selecting one or more of the candidate alignments as an optimal alignment or optimal alignments,based on the alignment scores.

The invention discloses a method for detecting a gene cassette array in a bacterium integron by using an EcoRII enzyme digestion map library, which comprises the following steps of: firstly, carrying out enzyme digestion on the gene cassette array by adopting the restriction enzyme EcoRII when a new screened gene cassette array is determined; comparing the gene cassette array with the constructed EcoRII enzyme digestion map library so as to determine the novelty of the gene cassette array; and selecting connection, transformation and sequencing analysis so as to realize purposeful sequencing if maps in the library are not matched with the gene cassette array. The method is accurate, rapid and economic and is convenient for information sharing. The method is more suitable for relevant departments such as hospitals, quarantine inspection, forecast, preventive treatment and the like to realize the effective monitoring and prevent the outbreak prevalent of drug-resistant bacteria caused by the horizontal transferring and spreading of the drug-resistant bacteria containing the integron under the condition that antibiotic misuse is not well restrained.

The present invention belongs to the field of Chinese medicine material quality identifying technology, and aims at providing one kind of PCR-RFLP method for identifying fritillary bulb and similar medicine material accurately. PCR amplification adopts the primer series including P1:5'-CGT AAC AAG GTT TCC GTA GGTGAA-3' and P2: 5' -GCT ACG TTC TTC ATC GAT-3'; the characteristic base sequence of fritillary bulb is 5'-TGCCCGCCCTGCCCGGGACCTCGC-3'; and the restriction endonuclease Sma I and its isoschizomer can identify and incise the sequence. The identification process includes: extracting medicine DNA, PCR amplification with the primers P1 and P2, digesting the PCR product with restriction endonuclease Sma I, agarose gel electrophoresis to obtain the analysis result, compared with fritillary bulb PCR-RFLP characteristic result to judge whether the sample is fritillary bulb.

The invention provides a polymerase chain reactino-restrictive enzyme-cut chart molecule (PCR-RFLP) method accurately identifying honeysuckle in genuine producing areas (Henan, Shandong) and nongenuine producing areas (other producing areas). The characteristic DNA alkali sequence of honeysuckle in genuine: 5'-GCCCCCCCGC CCCGCCTCCC ACAGGGTCGC G-3'; restrictive inner cut enayme EcoNi and its same cut-enzyme can identify and cut this sequence. The identifying course: extracting DNA of medical materials; using a pair of guide matters to make PCR increase; using restrictive inner cut enayme EcoNI and its same cut enayme to digest PCR product; analyzing the result by using gelation and electrophoresis of gelose; in contrast with the characteristic result of PCR-RFLP of genuine honeysuckle, judging if the tested product is genuine honeysuckle.

Disclosed is a PCR-RFLP identification method for different subgroups of sugarcane white leaf disease phytoplasma, wherein a tuf gene of a sugarcane white leaf disease phytoplasma is taken as an object for designing specific primers, a tuf gene fragment is obtained by PCR amplification, and a restriction endonuclease Msp I is then used to digest the tuf gene fragment obtained by amplification, and different subgroups of the sugarcane white leaf disease phytoplasma are distinguished by a differentiated RFLP restriction map. Therefore, a sugarcane white leaf disease phytoplasma subgroup 16SrXI-B and a sugarcane white leaf disease phytoplasma subgroup 16SrXI-D can be identified without sequencing.