DNA Analysis Services and Software www.sequentix.de

Sequence awareness

Our customer service:

  • In defined intervals we search public sequence databases and deliver all relevant sequences and associated data to our customers.
  • We do the query and our customers are up-to-date!
  • We deliver a start-up result of a database query (e.g. GenBank) with all available sequences.
  • Regular upgrades including recently published sequences.
  • Regular updates of actualised database entries.

Our customers provide:

  • Information about their field of interest (genes, organisms, sequence motifs, etc.)
  • Desired updating interval (weekly, monthly, every 3 months)
  • Desired data format: GenBank, database.



What does "molecular sequence awareness" refer to?
  • Sequence databases, e.g. NCBI's GenBank or the EMBL database, are large data storages which change with respect to their content. They are not static, i.e. every day new data is deposited into these databases and old records are updated upon receipt of new data. The daily changes of database content necessitate a high flexibility and special skills of the end-users. Therefore, scientists who want to incorporate actual sequence data in their publications are faced with the problem that they have to query public databases quite frequently otherwise they risk to deal with obsolete data. Finding the appropriate data in public databases is a time-consuming process.
  • An example:
    A scientist would like to reconstruct the evolution of some organisms based on analyses of their 16S rRNA or 18S rRNA gene sequence. To obtain an almost complete overview on the appropriate sequences he has to query public databases for at least the following expressions: '18S rRNA gene', '18S rDNA', 'small subunit ribosomal DNA', 'small subunit ribosomal RNA gene', 'SSU rRNA gene', 'SSU rDNA', etc.
    After download the scientist has to sort out completely new records from preexisting ones. In order to discover changes a comprehensive comparison of the recently downloaded data with preexisting data (previously downloaded) is necessary.
  • Sequence awareness is important in order to keep your sequence alignments and phylogenetic conclusions up to date.
  • This problem can be circumvented by using the SequentiX sequence awareness and updating service.

Keywords: sequence awareness, sequence update, upgrade, GenBank, changes, documentation, database, alignment, up-to-date
SequentiX - Digital DNA Processing
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D-18249 Klein Raden
Germany
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