IC Bioinfs/Project1/Das Reference Server

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Our Reference Server

  • Basically, the DAS reference server provides with capabilities to query the data on:
    • Entry Points-The way I understood this, will be the IDs of the parts we are working with.
    • Features- The list of features that one particular part has.
    • Sequence- The sequence of the part

More features can be added.

A list of DAS commands

These are the commands for the main features of our DAS Ref Server.You can play with those, once we have the DAS server live, otherwise, if you are really keen, you can follow the tutorial on setting up a das server and then just copyingthe classes I wrote, but I think there are more urgent things to work on. At the moment, the information is obtained from the DB at codon, using the SQL queries shown below. I tested this classes on my Tomcat server. Obviously,all this will have to be changed when the new database(in bioSQL is done).

  • Features request:

Uses getFeatures(Segment seg, String[] types), getFeatures(String reference) Lists all the features of a given part Parameters : PI_ID:start,end

Example, for first part: Using the SQL query: "SELECT feat_ID FROM seq_feat WHERE PI_ID =1


  • Sequence request:

Uses method getSequence

Returns the sequence of a given part(in ref)

Example, for part with PI_ID =1 Uses SQL query:"SELECT sequence FROM parts_info where PI_ID = 1 http://localhost:8080/DAS/myPlugin/sequence?segment=1

  • Entry Points request:

Uses methods getEntryPoints and getLandmarkLength

getEntryPoints creates a set with all the PI_IDs, which goes to unknown workings of other DAS classes. Then, in getLandmarkLength, a call to the DB("SELECT size FROM parts_info WHERE PI_ID="+ ref) retrieves all the sizes from the PI_IDs given on the previous method

  • The MIT provides with:
<SEGMENT id="BBa_R0050" size="55" start="1" stop="55" orientation="+" subparts="no">BBa_R0050</SEGMENT>
  • And our DAS server only has:
<SEGMENT id="1" size="999" subparts="no" />

But more details can be added later if needed.

Definition of a Reference Server

From JavaDoc directly:(will add more info later) A DAS reference source is very similar in most respects to an annotation source. In protocol terms, the two substantive differences are:

  • Reference servers serve DNA sequence as well as features
  • Reference servers offer a list of `entry points' -- the top level sequences in the database

The extra methods on this interface reflect the need to serve this extra data. In addition, reference servers may serve information about how sequence fragments (e.g. clones) are assembled into larger structures (e.g. contigs). If present, assembly information should be communicated by including BioJava ComponentFeature objects in the feature table. These are automatically translated by Dazzle into DAS category=component features.