摘要:

AbstractWe evaluate current levels of accuracy for estimation of molecular weight (Mr) and isoelectric point (pI) to proteins on two‐dimensional (2‐D) gels as well as the distribution and clustering of proteins in the predicted proteome ofE. coli. We also examine the ability to find single candidates within the predicted proteome for matching to a protein seen on 2‐D gels, based on the current level of accuracy. We discuss the levels of accuracy needed to match predicted proteins to observed proteins based solely onMrand pIcriteria obtained from genomic information, and propose methodology to achieve this level of accuracy. In addition, we will address the future goals of this work since the small genomes of bacteria provide a foundation and stepping stone to similar studies in higher orga

ISSN:0173-0835    

DOI:10.1002/elps.1150181503

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractAn algorithm for the representation of amino acid sequences as two‐dimensional point patterns (2‐D plot) is described. The algorithm is based on chaos game representation (CGR) for DNA sequences and was extended for amino acid sequences. The 2‐D plot depicts the sequentiality of amino acids and the amino acid composition of a protein. Changes in a protein sequence as insertion, deletion and repeats of amino acids are characterized by specific geometrical properties and changes in the 2‐D plots. The 2‐D plot may be considered as a two‐dimensional “fingerprint” of a protein. The properties of the algorithm are explained by user‐defined amino acid sequences. As an example the 2‐D plots of two selected heart proteins are generated. The sequences of these proteins are obtained from the protein sequence

ISSN:0173-0835    

DOI:10.1002/elps.1150181504

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractComparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS‐MODEL, a server for automated comparative protein modeling and of the SWISS‐PdbViewer, a sequence to structure workbench. The Swiss‐PdbViewer not only acts as a client for SWISS‐MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS‐MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experime

ISSN:0173-0835    

DOI:10.1002/elps.1150181505

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractAlthough two‐dimensional electrophoresis (2‐DE) computer analysis software packages have existed ever since 2‐DE technology was developed, it is only now that the hardware and software technology allows large‐scale studies to be performed on low‐cost personal computers or workstations, and that setting up a 2‐DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2‐DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2‐DE analysis software packages has now come to maturity. It can be run on a variety of low‐cost, general‐purpose personal computers, thus making the purchase of a 2‐DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2‐D PAGE, developed at the University Hospital of Geneva, is such a third‐generation software system for 2‐DE analysis. Based on unique image processing algorithms, this user‐friendly object‐oriented software package runs on multiple platforms, including Unix, MS‐Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state‐of‐the‐art image comparison, statistical data analysis facilities, and is Internet‐ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for

ISSN:0173-0835    

DOI:10.1002/elps.1150181506

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractAfter two generations of software systems for the analysis of two‐dimensional electrophoresis (2‐DE) images, a third generation of such software packages has recently emerged that combines state‐of‐the‐art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artifical intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2‐D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appelet al.; Electrophoresis1997,18,

ISSN:0173-0835    

DOI:10.1002/elps.1150181507

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractThe interpretation of two‐dimensional gel electrophoresis spot profiles can be facilitated by statistical and machine learning programs. Two different approaches to classification of spot profiles – cluster analysis and neural networks – are discussed. Neural networks for two different model patterns were designed and an algorithm for training of the net for the classification was developed. It was shown that the performance of neural networks is higher compared to cluster and principal component analysis. The possibility of combining both approaches into one process can increase reliability and speed of classification. Artificially created training sets with added random noise can be used for network training. The analysis was applied on theStreptomyces coelicolordevelopmental two‐dimensional (2‐D) gel

ISSN:0173-0835    

DOI:10.1002/elps.1150181508

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractTwo‐dimensional electrophoresis (2‐DE) has become a highly reproducible protein separation technique that currently serves as the main basis for proteome research and in particular for protein identification. Also, the Internet provides large utilities for exchanging data, and we can observe increased interest among scientists to build remote 2‐DE databases, since many members of the concerned community are now able to access the data. By preparing the data and programs that are required to create a federated 2‐DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide W

ISSN:0173-0835    

DOI:10.1002/elps.1150181509

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractThe 2DWG meta‐database is a searchable database of two‐dimensional (2‐D) electrophoretic gel images found on the Internet. A meta‐database contains information about locating data in other databases – but not that data itself. This database was constructed because of a need for an enriched set of World Wide Web (WWW) locations (URLs) of 2‐D gel images on the Internet. These gel images are used in conjunction with the National Cancer Institute (NCI) Flicker Server to manipulate and visually compare 2‐D gel images across the Internet. User's gels may also be compared with those in the database. The 2DWG is organized as a spreadsheet table with each gel image being represented by a row sorted by tissue type. Data for each gel includes tissue type, species, cell‐line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists,etc.The 2DWG may be searched to find relevant subsets of gels. Searching is done using the dbEngine – a WWW database search engine which accesses selected rows of gels from the full 2DWG table. The 2DWG meta‐database is accessible on the WWW athttp://www‐lecb.ncifcrf.gov/2dwgDB/and the NCI Flicker server athttp://www‐le

ISSN:0173-0835    

DOI:10.1002/elps.1150181510

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractRapid access to well‐organized information about gene products is important for many studies that simulatenously monitor large sets of those factors, for example with electrophoretic methods. HotMolecBase and GeneCards, Internet resources that may be accessed from our Bioinformatics homepage athttp://bioinfo.weizmann.ac.il/, have been designed to address similar problems. GeneCards presents semi‐automatically collected information about all approved human genes and their products (with a focus on cellular functions and medical aspects), and offers a new kind of knowledge navigation guidance system that interactively guides the information‐seeking scientist to relevant information. On the other hand, HotMolecBase is a collection of more extensive hypertext fact sheets about a small set of medically interesting molecules (mainly proteins) that are regarded as especially promising targets for drug development. Together, both resources may help scientists world‐wide to find their way in the growing labyrinth of biomedical information on the World Wide Web. In the present article, we want to explain how these resources may be used by researchers who want to access information related to particular spots on two‐dimensional electrophor

ISSN:0173-0835    

DOI:10.1002/elps.1150181511

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY

摘要:

AbstractA cDNA library was prepared from BW 5147 murine lymphoma cells in λeccIII phage and randomly partitioned into 291 sectors, each with 800–1000 recombinant phage plaques. One sector was chosen for further characterization in terms of sensitivity to restriction endonuclease cutting. Aliquots of DNA preparations from this sector were treated withXhoI,SmaI,NcoI,PvuII,PstI,HindIII,EcoRI,BamHI, andApaLI before being used as templates in a cell‐free expression system. The polypeptide products were separated by two‐dimensional (2‐D) gel electrophoresis and radiofluorographs of the gels were submitted to computer‐aided image analysis. The matched patterns were inspected for the presence or absence of spots upon individual endonuclease treatments. Thereafter the results were integrated in a data matrix which served as a basis to construct “restriction tags” for all spots. These (restriction) tags are binary numbers termed “cut numbers” and are a representation of the set of recognition sequences which are (or are not) part of the coding sequence. From 493 sequences (visualized as 2‐D gel spots), 12 were not cut by any of the nine enzymes, while 45 were cut by all of them. The percentages of sequences resistant to enzyme treatment ranged between 17% and 77% forNcoI andXhoI, respectively. The enzyme treatments led to the appearance of a certain portion of “new spots”, probably products from truncated sequences. From 512 possible cut numbers, 136 were assigned to the 493 spots. Restriction tags are available to facilitate retrieval of cDNA clones from the (p

ISSN:0173-0835    

DOI:10.1002/elps.1150181512

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1997

数据来源: WILEY