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1.
A convenient and adaptable package of DNA sequence analysis programs for microcomputers 总被引:16,自引:13,他引:16 下载免费PDF全文
We describe a package of DNA data handling and analysis programs designed for microcomputers. The package is convenient for immediate use by persons with little or no computer experience, and has been optimized by trial in our group for a year. By typing a single command, the user enters a system which asks questions or gives instructions in English. The system will enter, alter, and manage sequence files or a restriction enzyme library. It generates the reverse complement, translates, calculates codon usage, finds restriction sites, finds homologies with various degrees of mismatch, and graphs amino acid composition or base frequencies. A number of options for data handling and printing can be used to produce figures for publication. The package will be available in ANSI Standard FORTRAN for use with virtually any FORTRAN compiler. 相似文献
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Altuna Akalin Matthias Kormaksson Sheng Li Francine E Garrett-Bakelman Maria E Figueroa Ari Melnick Christopher E Mason 《Genome biology》2012,13(10):R87
DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation,
cellular specification and cancer development. Here, we describe an R package, methylKit, that
rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and
hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample
quality visualization, differential methylation analysis and annotation features, thus automating
and simplifying many of the steps for discerning statistically significant bases or regions of DNA
methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically
significant regions of differential methylation and stratify tumor subtypes. methylKit is available
at http://code.google.com/p/methylkit. 相似文献
3.
We describe here a new strategy of fragment preparation for sequencing procedures using endlabelled DNA fragments as substrates (2,3) which is directly applicable to DNA fragments cloned into the Pst I site of pBR322, or in modified form, to inserts into the BamH I or Sal I site of the same plasmid. Ordered sets of subclones of predetermined overlap are are generated. These can be sequenced directly without further strand- or fragment separation steps. 相似文献
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R H Gross 《Nucleic acids research》1986,14(1):591-596
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ADSP-a new package for computational sequence analysis 总被引:3,自引:0,他引:3
A new protein sequence analysis package, ADSP, is described,of which the SOMAP ScreenOriented Multiple AlignmentProcedure forms an integral part. ADSP (Algorithms and DataStructures for Protein sequence analysis) incorporates facilitiesto generate potent pattern-recognition discriminators and offersfour algorithms with which to scan any NBRF format sequencedatabase: the package has been designed, in particular, to interfacewith the OWL composite sequence database, one of the largest,distributed non-redundant sources of sequence data of its kind.The system incorporates a powerful method for compound featureanalysis, which provides the basis for characterizing and predictingthe occurrence of complete protein superfamilies and for pinpointingthe emergence of related subfamilies. Used iteratively, theapproach allows diagnostic performance to be rigorously refinedand its efficacy to be assessed both qualitatively and quantitatively,and results in the generation of refined structural or functionalfeatures suitable for entry into a database: this compilationof characteristic signatures is distinct from, but complementaryto, widely used compendia of pattern templates such as PROSUE. 相似文献
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A comprehensive DNA sequence library is essential for identification with DNA barcodes 总被引:1,自引:0,他引:1
In this study we examine the possibility of utilising partial cox1 gene sequences as barcodes to identify non-biting midges (Diptera: Chironomidae). We analysed DNA from 97 specimens of 47 species in the genera Cladotanytarsus, Micropsectra, Parapsectra, Paratanytarsus, Rheotanytarsus, Tanytarsus and Virgatanytarsus with a main focus on Micropsectra, Parapsectra and Paratanytarsus. Our findings show that (1) cox1 is easily amplified from extracts from different life stages with the standard barcoding primers. (2) Although K2P-distances between con-specific sequences varied up to 4.9%, con-specifics clustered together with 91-100% bootstrap support in maximum parsimony analysis. This indicates that barcodes may be excellent tools to identify species that are already in a cox1 library. (3) Both neighbour joining and maximum parsimony failed to reconstruct monophyletic genera. Thus, if a well-matching cox1 sequence is not already available in the library, the prospects of approximately identifying an unknown taxon, even to the correct genus of subtribe Tanytarsina, are not good. 相似文献
8.
M I Kanehisa 《Nucleic acids research》1982,10(1):183-196
An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a large-scale database can be used for comparative studies on sequence and structural homologies in order to find unnoted information stored in nucleic acid sequences. 相似文献
9.
Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system. 相似文献
10.
Programs of the recently released Unix version of the GeneticsComputing Group (GCG) sequence analysis package can now be accessedvia a user-friendly hypertext-like navigation system, HYGCG.The resultant system organizes the diverse suite of programsinto logical groups, and provides a guide and explanation ofcommands. In addition, for users unfamiliar with the Unix operatingsystem, the program also provides a similar interface to commonlyused Unix commands. Options for personal customization and expansionto accommodate GCG extensions and other software are also provided.This system should be useful especially to the inexperiencedor infrequent user as context-sensitive on-line help is providedwithin this simple and consistent approach. Written in the Clanguage and using the curses and termcap libraries, the systemis easily portable to most Unix environments and has been madefreely available via anonymous file transfer protocol (FTP)through the Internet global computer network. No modificationof the GCG package is needed. 相似文献
11.
Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools. 相似文献
12.
PEPPLOT, a protein secondary structure analysis program for the UWGCG sequence analysis software package. 总被引:12,自引:4,他引:8 下载免费PDF全文
We describe a program for the analysis of protein secondary structure that operates with the Sequence Analysis Software Package of the University of Wisconsin Genetics Computer Group (UWGCG). The program produces both graphic and printed output. Structure prediction using the Chou and Fasman and Robson et al methods, and hydropathy analysis by the method of Kyte and Doolittle are included along with a simplified method of hydrophobic moment analysis. The power of the program is the coordinated presentation of many different kinds of structural information on the same plot. 相似文献
13.
Recently, it has been shown by Calladine (1982) and Dickerson (1983) that DNA distortions due to steric clashes between opposing purines and pyrimidines can be quantitated based upon four sum functions. The distortions involve helical twist, roll, torsion angle variations and propeller twist. It is the contention of the authors that these perturbations in structure act as information carriers for various external DNA interactions. This paper describes a system that incorporates these four rules and various other functions that permit the systematic interactive exploration for significant patterns as a consequence of these steric clashes. 相似文献
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A simple miniaturized gel system suitable for DNA sequencing is described. Small ultrathin polyacrylamide gels are cast, eight or more at a time, using standard microscope slides. Gels, ready to use, can be stored for approximately 2 weeks. Gels are run horizontally in a standard mini-agarose gel apparatus. Typical run times are 6-8 min. A novel sample loading system permits volumes of standard sequencing reactions as small as 0.1 microl to be analyzed. Sequencing ladders were visualized using 35S-labeled DNA by autoradiography and by colorimetric detection. Band resolution compares favorably with that of large gels. The methods introduced here serve as a step toward the miniaturization of DNA sequencing and are amenable to automated sample loading and detection. 相似文献
18.
Synthesis of the human insulin gene. Part IV. New synthetic deoxyribooligonucleotide adaptors and primer for DNA cloning and sequence analysis 总被引:1,自引:0,他引:1
S A Narang R Brousseau H M Hsiung W Sung R Scarpulla G Ghangas L Lau B Hess R Wu 《Nucleic acids symposium series》1980,(7):377-385
The chemical synthesis of four new deoxyribooligonucleotides to be used as adaptors in molecular cloning of DNA for expression studies is described. These are (i) start-adaptor, (ii) stop-adaptor, (iii) conversion adaptor to insert ribosomal binding site, and (iv) retrieving adaptor. We have also synthesized a 19-bases-long primer, 5'-TTGTAAAACGACGGCCAGT-3' to increase the speed of DNA sequence analysis and also demonstrated its application using single-stranded M13 DNa vector. 相似文献
19.
Deleage Gilbert; Clerc Francois F.; Roux Bernard; Gautheron Daniele C. 《Bioinformatics (Oxford, England)》1988,4(3):351-356
A simple microcomputer package is described to make the theoreticalanalysis of protein sequences. Several methods designed to comparetwo sequences, to model proteolytic reactions and to predictthe secondary structure, the hydro-phobic/hydrophilic regionsand the potential antigenic sites of proteins have been includedin an Apple II microcomputer software. The package comprises21 programs as well as the secondary structure database of Kabschand Sander (1983).
Received on November 24, 1987; accepted on March 8, 1988 相似文献
20.
I Duband-Goulet V Carot A V Ulyanov S Douc-Rasy A Prunell 《Journal of molecular biology》1992,224(4):981-1001
Nucleosome formation on inverted repeats or on some alternations of purines and pyrimidines can be inhibited in vitro by DNA supercoiling through their supercoiling-induced structural transitions to cruciforms or Z-form DNA, respectively. We report here, as a result of study of single nucleosome reconstitutions on a DNA minicircle, that a physiological level of DNA supercoiling can also enhance nucleosome sequence preference. The 357 base-pair minicircle was composed of a promoter of phage SP6 RNA polymerase joined to a 256 base-pair fragment containing a sea urchin 5 S RNA gene. Nucleosome formation on the promoter was found to be enhanced on a topoisomer with in vivo superhelix density when compared to topoisomers of lower or higher superhelical densities, to the nicked circle, or to the linear DNA. In contrast, nucleosomes at other positions appeared to be insensitive to supercoiling. This observation relied on a novel procedure for the investigation of nucleosome positioning. The reconstituted circular chromatin was first linearized using a restriction endonuclease, and the linear chromatin so obtained was electrophoresed as nucleoprotein in a polyacrylamide gel. The gel showed well-fractionated bands whose mobilities were a V-like function of nucleosome positions, with the nucleosome near the middle migrating less. This behavior is similar to that previously observed for complexes of sequence-specific DNA-bending proteins with circularly permuted DNA fragments, and presumably reflects the change in the direction of the DNA axis between the entrance and the exit of the particle. Possible mechanisms for such supercoiling-induced modulation of nucleosome formation are discussed in the light of the supercoiling-dependent susceptibility to cleavage of the naked minicircle with S1 and Bal31 nucleases; and a comparison between DNase I cleavage patterns of the modulated nucleosome and of another, non-modulated, overlapping nucleosome. 相似文献