Construction of restriction maps

Bellon, Bernard

doi:10.1093/bioinformatics/4.1.111

Cited by 16 publications

(4 citation statements)

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“…The nucleotide sequences were analyzed with computer programs developed by Bellon (6) and those associated with the BISANCE data base of the Centre Interuniversitaire de Traitement de l'Information (CITI2). Sequence comparisons were carried out with programs developed by Pustell and Kafatos (53,54) cDNA clones corresponding to the m region have been isolated from a young pupal cDNA library (51) and characterized (1).…”

Section: Methodsmentioning

confidence: 99%

A Drosophila rotund transcript expressed during spermatogenesis and imaginal disc morphogenesis encodes a protein which is similar to human Rac GTPase-activating (racGAP) proteins.

et al. 1992

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The rotund (rn) locus ofDrosophila melanogaster at cytogenetic position 84D3,4 has been isolated and cloned on the basis of the mutant phenotpe: an absence of structures in the subdistal regions of the appendages. The shortened appendages are the consequence of a localized cell death in the imaginal discs, precursors of the adult appendages. Physical characterization of the rn locus has demonstrated that it is relatively large, occupying a minimum of 50 kb. There are two major transcripts of 1.7 kb (ml.7) and 5.3 kb (m5.3). We present here the sequence analysis of ml.7 and its putative product, rnprotl.7, and show that rnprotl.7 is similar to the product of the human n-chimaerin gene, which is expressed in brain and testes. Recently, the GAP activity of n-chimaerin was demonstrated and shown to be specific for the Rac subfamily of the Ras oncoproteins. The Rac proteins have been implicated in the regulation of secretory processes. In addition to being expressed in the imaginal discs, the ml.7 racGAP transcript was detected in developmentally specific germ line cells of the testes, the primary spermatocytes.

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Section: Methodsmentioning

confidence: 99%

A Drosophila rotund transcript expressed during spermatogenesis and imaginal disc morphogenesis encodes a protein which is similar to human Rac GTPase-activating (racGAP) proteins.

et al. 1992

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“…Unfortunately, any attempt to reconstruct a restriction map from experimental data-i.e., the fragment sizes measured after gel electrophoresis, is impeded by experimental error (1)(2)(3)(4). Consequently, a mapping strategy will fail when fragment-length measurement is too inaccurate.…”

Section: Discussionmentioning

confidence: 99%

Algorithms for the restriction-site mapping of DNA molecules.

Krawczak¹

1988

Proc. Natl. Acad. Sci. U.S.A.

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Two algorithms are described that rapidly construct restriction maps of DNA molecules from single-and double-digest data. The implementation of these algorithms into the Pascal programs AMAPK and AMARD allows such mapping to be done on microcomputers.The restriction map of a DNA molecule-i.e., the number and positions of the restriction sites of various enzymes, is quite specific. When two 20-kilobase (kb) molecules are randomly chosen and digested with one and the same enzyme, assuming the recognition sequence ofthis enzyme to be 4 base pairs (bp) long, the chance ofobtaining two identical restriction maps is 1lO-17. Thus, the restriction map is useful for characterizing such molecules and may ground further analyses.In the present paper two algorithms are described that construct restriction maps rapidly from single-and doubledigest data. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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“…= 6.4 x 1015 different orders. Even assuming an unrealistically low error of I % in fragment sizes, no unique solution to the map could be found using a computer implementation of the 'branch and bound' approach (Fitch et al, 1983;Nolan et al, 1984;Bellon, 1988;Krawczak, 1988;Tuffery et al, 1988). Therefore we had to include data from partial digestion with SmaI (Table 1) and of sequential digestion by SstII followed by SmaI (with sizing on two-dimensional gels; Fig.…”

Section: Restriction-mapping Of Chromosome IIImentioning

confidence: 99%

“…It would be a great advantage, then, if computer programs were available which could solve the map solely using this easily obtained data. However, even if the formidable computational problems can be overcome (Stefik, 1978;Pearson, 1982;Fitch et al, 1983;Durand & Bregegere, 1984;Nolan et al, 1984;Polner et al, 1984;Allison & Yee, 1988;Bellon, 1988;Krawczak, 1988;Tuffery et al, 1988), a unique solution seldom exists for maps of > 10 fragments (Durand & Bregegere, 1984;Nolan et al, 1984;Allison & Yee, 1988;Krawczak, 1988). More complex data are needed to resolve inevitable ambiguities.…”

Section: Mapping Inserts In Yacsmentioning

confidence: 99%

Cellular gels. Purifying and mapping long DNA molecules

Dear¹,

Cook²

1991

Biochemical Journal

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Long DNA molecules of greater than 10(5) bp (0.1 Mbp) are easily broken by pipetting. Therefore, chromosomal DNA is generally isolated after embedding cells in a protective coat of agarose. The embedded DNA can then be cut into long pieces and fractionated on gels using pulsed fields, but these pieces are again easily broken if the resolved DNA molecules are recovered from the gels. We now describe a novel gel matrix, a 'cellular' gel, that permits the recovery of resolved fragments from gels in a form that enables facile manipulation without shear. This facilitates purification and restriction mapping of fragments of 0.1-1.0 Mbp. We illustrate the utility of the method by mapping chromosome III of baker's yeast, which has a length of approximately 0.36 Mbp. This method should facilitate purification and restriction mapping of yeast artificial chromosomes.

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Construction of restriction maps

Cited by 16 publications

References 0 publications

A Drosophila rotund transcript expressed during spermatogenesis and imaginal disc morphogenesis encodes a protein which is similar to human Rac GTPase-activating (racGAP) proteins.

A Drosophila rotund transcript expressed during spermatogenesis and imaginal disc morphogenesis encodes a protein which is similar to human Rac GTPase-activating (racGAP) proteins.

Algorithms for the restriction-site mapping of DNA molecules.

Cellular gels. Purifying and mapping long DNA molecules

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