Searching NEMBASE
We have provided three ways in which you can search the NEMBASE database by web based forms. These include :
  1. Annotation - searching for keywords in blast output.
  2. Sequence similarity - via a blast web interface.
  3. Stage specificity - searching for explicit expression patterns.
The details for each page is listed below.
Searching by Annotation
This page provides a way of searching the cluster dbs by annotation derived from precomputed blast searches (blastn vrs nr, blastx vrs nr and blastn vrs dbest).
  1. Select the 'Organism' db to search against.
  2. Enter the keyword you wish to search for in the text box under ' Search against blast output' (e.g. collagen etc).
  3. 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).
  4. Output can ordered either by abundance of ESTs in the cluster or by blast score by clicking the appropriate option.
  5. To submit your request, click the button marked submit.
    Alternatively you may retreive specific clusters by entering the cluster number in the text box at the top of the page.

    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. Select the 'Organism' db you wish to blast against
  2. Choose the appropriate 'Program' and options.
  3. Enter your sequence in FASTA format and select your appropriate output view options.
  4. 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 enables you to search for clusters on the basis of stage specificity. At the moment this is only available for the Brugia clusters, but will be expanded once we have gathered enough data. To use this page simply enter values into the boxes which you want to limit your search for. e.g. if you wanted to find clusters which contained ESTs from the L4 stage but not in the infective L3 stage you would enter '>0' into the box marked 'L4' and '0' in the box marked 'Total infective L3'. The form recognises numbers and '>' and '<' symbols.