News Overview Construction Searching Cluster Info. Protein Info. SimiTri Conf


General

We have provided three ways in which you can search the TardiBASE database by web based forms. These are :
  • Cluster name or Genbank Accession number.
  • Annotation - searching for keywords in blast output.
  • Sequence similarity - via a blast web interface.
    •  The details for each search are listed below.
    Searching by Cluster name or accession number

    This page provides a way of searching the cluster databases by the name of a H.dujardini cluster or searching for a single known EST by its Genbank accession number. It will direct you to the relevant cluster containing your EST and any other H.dujardini EST we have clustered with it.
    1. Enter the HDC cluster name OR Genbanks accession number in the text box
    2. To submit your request, click the button marked submit.

    After a few moments the information available for your cluster will be displayed,
    Searching by Annotation

    This page provides a way of searching the cluster databases by anontation derived from precomputed blast searches (blastn vrs nr, blastx vrs nr and blastn vrs dbest).
    1. Enter the keyword you wish to search for in the text box (e.g. collagen etc).
    2. If you want to limit the accuracy of the blast hits you may enter the e-score exponent in the 'Minimum e-score box' (e.g. if you wanted only hits < e^-30 you would enter '30' in this box).
    3. Output can ordered either by abundance of ESTs in the cluster or by blast score by clicking the appropriate option.
    4. To submit your request, click the button marked submit.

      After a few moments a list of clusters matching your request will be displayed, by clicking on the cluster number you will bring up the available information for that cluster.
    Searching by Sequence Similarity

    This page allows you to retrieve clusters which bear sequence similarity to a specified sequence using BLAST.
    1. Choose the appropriate 'Program' and options.
    2. Enter your sequence in FASTA format and select your appropriate output view options.
    3. Click on 'Search' to perform your BLAST.
      After a few moments you will see the blast output, again, by clicking on the cluster number, you will bring up the available information for that cluster.
    Searching by Stage Specificity

    This page will enable you to search for clusters on the basis of life stage specificity. Curently TardiBASE only contains clusters from mixed stage libraries so the facility is not required. We hope to make it available as clusters from other libraries are added to the database.