The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases Public Deposited

http://ir.library.oregonstate.edu/concern/defaults/jd472x35s

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • Background: Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist. Results: We present the Personal Sequence Database (PSD), a suite of tools to create and maintain small- to medium-sized web-accessible sequence databases. All interactions with PSD tools occur via the internet with a web browser. Users may define sequence groups within their database that can be maintained privately or published to the web for public use. A sequence group can be downloaded, browsed, searched by keyword or searched for sequence similarities using BLAST. Publishing a sequence group extends these capabilities to colleagues and collaborators. In addition to being able to manage their own sequence databases, users can enroll sequences in BLASTAgent, a BLAST hit tracking system, to monitor NCBI databases for new entries displaying a specified level of nucleotide or amino acid similarity. Conclusion: The PSD offers a valuable set of resources unavailable elsewhere. In addition to managing sequence data and BLAST search results, it facilitates data sharing with colleagues, collaborators and public users. The PSD is hosted by the authors and is available at http:// bioinfo.cgrb.oregonstate.edu/psd/.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Givan, S. A., Sullivan, C. M., Carrington, J. C. (2007). The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases. BMC a, 8(479)
Academic Affiliation
Series
Rights Statement
Funding Statement (additional comments about funding)
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Submitted by Mary Phan (mpscanner@gmail.com) on 2011-02-04T18:11:17Z No. of bitstreams: 1 1471-2105-8-479.pdf: 763152 bytes, checksum: a7dbac1ef87e2408e7a8d791c835e20d (MD5)
  • description.provenance : Made available in DSpace on 2011-02-15T01:58:23Z (GMT). No. of bitstreams: 1 1471-2105-8-479.pdf: 763152 bytes, checksum: a7dbac1ef87e2408e7a8d791c835e20d (MD5) Previous issue date: 2007-12-18
  • description.provenance : Approved for entry into archive by Sue Kunda(sue.kunda@oregonstate.edu) on 2011-02-15T01:58:23Z (GMT) No. of bitstreams: 1 1471-2105-8-479.pdf: 763152 bytes, checksum: a7dbac1ef87e2408e7a8d791c835e20d (MD5)

Relationships

In Administrative Set:
Last modified: 07/11/2017

Downloadable Content

Download PDF
Citations:

EndNote | Zotero | Mendeley

Items