Dataset Information

Integrated databanks access and sequence/structure analysis services at the PBIL.

ABSTRACT: The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

SUBMITTER: Perriere G

PROVIDER: S-EPMC168937 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature

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Integrated databanks access and sequence/structure analysis services at the PBIL.

Perrière Guy G Combet Christophe C Penel Simon S Blanchet Christophe C Thioulouse Jean J Geourjon Christophe C Grassot Julien J Charavay Céline C Gouy Manolo M Duret Laurent L Deléage Gilbert G

Nucleic acids research 20030701 13

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological in ...[more]

PMID: 12824334

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Project description:BackgroundComparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.ResultsThe molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.ConclusionThe tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera.

Project description:PROBLEM: The hospital based musculoskeletal service in northwest Wales was unable to cope with the demand for referrals from general practitioners. Waiting times were long, duplicate referrals to other departments were common, and general practitioners were reluctant to refer patients with common problems because of the perceived lack of service. Many referrals were made to the inappropriate specialty, especially orthopaedics. At least part of this problem was due to a lack of coordination between the four hospital departments providing musculoskeletal services and the emphasis on district general hospital based rather than community provision. DESIGN: Review over 18 months of impact of the targeted early access to musculoskeletal services (TEAMS) programme on accessibility to musculoskeletal services. SETTING: Northwest Wales. KEY MEASURES FOR IMPROVEMENT: Number of patients referred and seen with musculoskeletal problems, waiting times, number of duplicate referrals, and surgery conversion rates in orthopaedic clinics. STRATEGIES FOR CHANGE: Establishing with central clinical triage a common pathway for all musculoskeletal referrals so that patients attend the appropriate department. A back pain pathway led by extended scope physiotherapists was developed, and general practitioners with special interests and extended scope physiotherapists were trained to provide services for patients with uncomplicated musculoskeletal problems in the community. EFFECTS OF CHANGE: Over 18 months the number of referrals more than doubled. Despite this, waiting times for musculoskeletal services fell; this was noticeable for rheumatology and pain management. Duplicate referrals were abolished. Surgery conversion rates did not, however, change. Questionnaires from the clinics showed a high level of patient satisfaction. LESSONS LEARNT: Integration of hospital services that traditionally have worked in isolation can result in greatly improved access to musculoskeletal services. Community based multidisciplinary clinics run by specially trained general practitioners with special interests and extended scope physiotherapists are an effective way of managing patients with uncomplicated musculoskeletal problems and have been well received by patients and general practitioners. The huge unmet burden of need was reflected by the great increase in musculoskeletal referrals. Other approaches are needed to meet this, including better education of general practitioners and methods for identifying and modifying psychosocial risk factors for chronic pain at an early stage.

Dataset Information

Integrated databanks access and sequence/structure analysis services at the PBIL.

Publications

Integrated databanks access and sequence/structure analysis services at the PBIL.

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