Sequences of six genes and several open reading frames in the kinetoplast maxicircle DNA of Leishmania tarentolae.
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The DNA sequence of approximately 80% of the transcribed region of the kinetoplast maxicircle DNA of Leishmania tarentolae was obtained, and structural genes were localized by comparison of the translated amino acid sequences with those of known mitochondrial genes from other organisms. By this method, the genes for cytochrome oxidase subunits I, II, and III, cytochrome b, and human mitochondrial unidentified reading frames 4 and 5 were identified. By comparing the amino acid sequences of the putative L. tarentolae genes with those of known genes, we conclude that TGA codes for tryptophan, as in most other mitochondrial systems. This is the only apparent change from the universal genetic code. The six identified structural genes show various degrees of divergence from the homologous genes in other species, with cytochrome oxidase subunit I being the most conserved and cytochrome oxidase subunit III being the least conserved. A comparison of the cytochrome b genes from L. tarentolae and Trypanosoma brucei showed that the ratio of transversions to transitions is 1:1, suggesting that these species diverged from each other more than 80 X 10(6) years ago. Several as yet unidentified open reading frames were also present in the maxicircle sequence. These data confirm that maxicircle DNA has a coding potential which typifies other mitochondrial systems. (+info)
A computer program for the management of small cosmid banks.
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A Fortran program has been written to permit comparative analysis of Grunstein-Hogness hybridisation data from small plasmid or cosmid banks. This program is particularly useful for restriction mapping using genome walking techniques and will facilitate the analysis of genomes in the 200 kb to 5000 kb size range. (+info)
PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic display of conventional restriction maps.
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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. (+info)
Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments.
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A stand-alone, interactive computer system has been developed that automates the analysis of ethidium bromide-stained agarose and acrylamide gels on which DNA restriction fragments have been separated by size. High-resolution digital images of the gels are obtained using a camera that contains a one-dimensional, 2048-pixel photodiode array that is mechanically translated through 2048 discrete steps in a direction perpendicular to the gel lanes. An automatic band-detection algorithm is used to establish the positions of the gel bands. A color-video graphics system, on which both the gel image and a variety of operator-controlled overlays are displayed, allows the operator to visualize and interact with critical stages of the analysis. The principal interactive steps involve defining the regions of the image that are to be analyzed and editing the results of the band-detection process. The system produces a machine-readable output file that contains the positions, intensities, and descriptive classifications of all the bands, as well as documentary information about the experiment. This file is normally further processed on a larger computer to obtain fragment-size assignments. (+info)
GELYSIS: Pascal-implemented analysis of one-dimensional electrophoresis gels.
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GELYSIS (GEL analYSIS) is a Pascal implementation of an algorithm that takes data on the distances migrated by DNA fragments in a one-dimension electrophoretic gel and calculates the sizes of the fragments based on the known sizes of marker fragments. A key step in the overall algorithm is a cubic-spline best-fit of marker calibration data. An option of the program is the generation of graphic representations of the gel and of the calibration spline that are convenient for primary data storage or for publication. Provision is made for specifying different band intensities in the graphic output of the gel. (+info)
Integrated library systems.
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The development of integrated library systems is discussed. The four major discussion points are (1) initial efforts; (2) network resources; (3) minicomputer-based systems; and (4) beyond library automation. Four existing systems are cited as examples of current systems. (+info)
Computer methods to locate signals in nucleic acid sequences.
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This paper describes computer methods for locating signals in nucleic acid sequences. The signals include ribosome binding sites, promoter sequences and splice junctions. The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences. (+info)
Graphic methods to determine the function of nucleic acid sequences.
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We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effects that coding for a protein has on the coding sequence, to locate tRNA genes by looking for secondary structure and conserved bases, and methods to locate signals such as promoters. Techniques to identify unusual regions of sequence and to search for potential Z DNA-forming regions are also included. Most of the routines produce graphical output which gives ease of interpretation and allows superposition of several independent forms of analysis. (+info)