Bioinformatics — principles and potential of a new multidisciplinary tool

Benton, David

doi:10.1016/0167-7799(96)10037-8

Cited by 82 publications

(39 citation statements)

References 79 publications

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“…However, the readiness with which sequence information can be utilized is often hampered by limited annotation. The number of unclassified genes is steadily increasing, and there is a need for new tools for functional and structural classification of genes and gene products (4). The use of specific and sensitive patterns is one way to classify putative proteins into groups or families.…”

Section: Discussionmentioning

confidence: 99%

Improved Pattern for Genome-Based Screening Identifies Novel Cell Wall-Attached Proteins in Gram-Positive Bacteria

Janulczyk

Rasmussen

2001

Infect Immun

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With a large number of sequenced microbial genomes available, tools for identifying groups or classes of proteins have become increasingly important. Here we present an improved pattern for the identification of cell wall-attached proteins (CWPs), a group of proteins with diverse and important functions in gram-positive bacteria. This tripartite pattern is based on analysis of 65 previously described cell wall-attached proteins and takes into account the three principal requirements for cell wall sorting; a sortase target region (LPXTGX), a membrane-spanning region, and a charged stop-transfer tail. In five different genomes of gram-positive bacteria, the tripartite pattern identified a total of 35 putative CWPs, 19 of which were novel. The specificity and sensitivity of the tripartite pattern are higher than those of the classical pattern, which is based solely on the sortase target region. Several putative CWPs with atypical sortase target regions were identified. In the complete genome of the important human pathogen Streptococcus pyogenes, the tripartite pattern identified 14 putative CWPs. Seven of the putative S. pyogenes proteins were novel, and two of these were a 5 nucleotidase and a pullulanase. This study represents the first whole-genome screening for CWPs, and we conclude that the tripartite pattern is highly suitable for this purpose. Identification of CWPs using this pattern offers important possibilities in the study of the pathogenesis and physiology of gram-positive bacteria.

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Section: Discussionmentioning

confidence: 99%

Improved Pattern for Genome-Based Screening Identifies Novel Cell Wall-Attached Proteins in Gram-Positive Bacteria

Janulczyk

Rasmussen

2001

Infect Immun

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“…Datasets acquired with these high-performance imaging devices have the global characteristic to improve resolutions in both time and space. These technological advances have operated in two distinct ways: acquisition dedicated devices and image analysis programs [e.g., Benton, 1996]. A correlate of this obvious fact is the growing amount of collected data.…”

Section: Introductionmentioning

confidence: 99%

B-SPID: An object-relational database architecture to store, retrieve, and manipulate neuroimaging data

et al. 1999

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We propose a hardware and software architecture to respond to crucial problems in the neuroimaging field: storage, retrieval, and processing of large datasets. The B-SPID project, here discussed, concerns the processing of neuroimages and attached components stored in an object-relational multimedia database management system (DBMS). Advanced bioinformation concepts are exploited in this project such as large scale data storage, high level graphical user interfaces and 3D graphical processing and display of data. Our database implementation is based on standard programming components, runs on several UNIX platforms and is written to be evolutive. Queries on this database are designed to obtain and display from neuroimaging data several types of results (pictures, text, or 3D graphical shapes) on heterogeneous systems.

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“…Areas which will not be discussed and for which the reader is directed to recent reviews or references include gene expression profiling in situ, 6 protein expression profiling using 2D gels and mass spectrometry analysis, 7-9 parallel cellular and nucleic acid sample preparation, [10][11][12] and bio-informatics approaches to data processing and interpretation. [13][14][15] …”

Section: Introductionmentioning

confidence: 99%

Parallel molecular genetic analysis

et al. 1998

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We describe recent progress in parallel molecular genetic analyses using DNA microarrays, gel-based systems, and capillary electrophoresis and utilization of these approaches in a variety of molecular biology assays. These applications include use of polymorphic markers for mapping of genes and disease-associated loci and carrier detection for genetic diseases. Application of these technologies in molecular diagnostics as well as fluorescent technologies in DNA analysis using immobilized oligonucleotide arrays on silicon or glass microchips are discussed. The array-based assays include sequencing by hybridization, cDNA expression profiling, comparative genome hybridization and genetic linkage analysis. Developments in non microarraybased, parallel analyses of mutations and gene expression profiles are reviewed. The promise of and recent progress in capillary array electrophoresis for parallel DNA sequence analysis and genotyping is summarized. Finally, a framework for decision making in selecting available technology options for specific molecular genetic analyses is presented.

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Bioinformatics — principles and potential of a new multidisciplinary tool

Cited by 82 publications

References 79 publications

Improved Pattern for Genome-Based Screening Identifies Novel Cell Wall-Attached Proteins in Gram-Positive Bacteria

Improved Pattern for Genome-Based Screening Identifies Novel Cell Wall-Attached Proteins in Gram-Positive Bacteria

B-SPID: An object-relational database architecture to store, retrieve, and manipulate neuroimaging data

Parallel molecular genetic analysis

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