Quantcast
Viewing all articles
Browse latest Browse all 41826

Retrieving results using BLAST SOAP API

Hi ;

I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:

"blasp.exe -query input.txt -db pdbaa -evalue 0.01 -out output.txt"

Now I am moving to using the SOAP API (in C# language). I query using the following method using Blast4queuesearchrequestlite:

        public static string SubmitSearchLite(){
        Blast4queuesearchrequestlite blreq = new Blast4queuesearchrequestlite();
        blreq.databasename = "pdb";
        blreq.query = @">MyData KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIIL"
        blreq.options = new Blast4queuesearchrequestliteOptions();
        blreq.options.Blast4optionslite = new Blast4optionslite();    
        blreq.options.Blast4optionslite.task = "blastp";
        blreq.options.Blast4optionslite.options = new Blast4optionsliteOptions();
        blreq.options.Blast4optionslite.options.Blast4commonoptions = new Blast4commonoptions();
        blreq.options.Blast4optionslite.options.Blast4commonoptions.evalue = 0.01;

        Blast4queuesearchreply reply = m_WebService.SubmitSearchLite(blreq);
        x_HandleVerboseOutput(blreq, reply);}

My first problem is that this works but the evalue is not working. It returns all the proteins with any evalues up to 10.(which is the default).

Then, I try to get the results as below:

  public static void GetResults(String RID)
        {
            Blast4getsearchresultsrequest blreq = new Blast4getsearchresultsrequest();
            blreq.requestid = RID;
            Blast4getsearchresultsreply reply = m_WebService.GetSearchResults(blreq);
            x_HandleVerboseOutput(blreq, reply);
            const String fname = @"results.xml";
            x_SerializeAsXml(fname, reply);
        }

My second problem is that, what I get as result is an XML which does not contain any information about the PDB codes of the results in hit table: such as which i used to get with command line:

 pdb|1A19|A  Chain A, Barstar (Free), C82a Mutant >pdb|1A19|B Chai...   182    3e-047 
 pdb|3DA7|C  Chain C, A Conformationally Strained, Circular Permut...   181    1e-046 
 pdb|1AY7|B  Chain B, Ribonuclease Sa Complex With Barstar >pdb|1B...   180    1e-046

Can you please guide me on these 2 problems: 1) setting the evalue in query 2) Retrieving the hit table (with pdb codes as result.)

Thanks;


Viewing all articles
Browse latest Browse all 41826

Trending Articles