Issues and Problems with Blast workflows

BLASTN

(Note all these tests were done using the TavernaScuflWorkbench^? version win32-0.1beta6 )

Test_XLRHODOP

XScufl file emblAccNumberXLRHODOPseqretBlastn.xml This blastn_ncbi example uses the embl entry XLRHODOP as its test input.

• For the full sequence 1684 letters (trim_from set to 1), a complete blast result was obtained in approx 5 mins
  • Result (748K) blastn_res_XLRHODOP.txt
    • http://twiki.mygrid.org.uk/twiki/pub/Mygrid/EmbossTests/blastn_res1.txt is a previous result of blasting XLRHODOP sequence from EmbossTests using an older WSFL workflow and Soaplab
• For a shortened sequence 1084 letters (trim_from set to 601), an empty result set was returned after about 4 mins,
  • this shortened sequence was accepted by the web interface for blastn - NCBI blastn

Test_X07024

XScufl file emblAccNumberX07024seqretBlastn.xml This blastn_ncbi example uses the embl entry X07024 as its test input.

• For the full sequence 5257 letters, an empty result set was returned after about 7 mins
  • Result blastn_res_x07024.txt: example empty result
• A shortened sequence of 2650 letters, did give a result from the NCBI web interface - NCBI blastn

Test_User_Sequence

XScufl file : sequenceBlastn.xml

This blastn_ncbi example allows the user to paste in a sequence. Its results were the same as the examples that involved using seqret to get a test sequence. XLRHODOP is the only sequence for which results have been obtained.

Empty results

On several examples the blastn processor appears to complete but the results are incomplete. For example note that there is no done at the end of the line Searching.... in the example below.

BLASTN 2.2.2 [Dec-14-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 
         (5257 letters)

Database: embl 
           3,078,285 sequences; 555,853,030 total letters

Searching.....................................................

( From blastn_res_x07024.txt: example empty result )

Comparison Soaplab and Web Blastn

Versions and databases differ

The NCBI blastn web interface gives (05 Nov 2003) e.g. NCBI_BLAST_example.htm

• BLASTN 2.2.6 [Apr-09-2003]
• Database: All GenBank^?+EMBL+DDBJ+PDB sequences
• Posted date: Nov 4, 2003 10:45 PM, Number of letters in database: -24,371,552, Number of sequences in database: 1,698,194

The Soaplab NCBI blastn web service gives (05 Nov 2003) e.g. blastn_res_XLRHODOP.txt

• BLASTN 2.2.2 [Dec-14-2001]
• Database: embl
  • others available through database parameter, see description_blastn.xml in ExampleEmbossDescriptions for the list.
• Posted date: Sep 4, 2003 3:04 PM, Number of letters in database: 555,853,030, Number of sequences in database: 3,078,285

Scope of results

An example result for blastn using the NCBI web interface, with the default parameters, includes some identifiers that do not appear to be valid for seqret. For example, XM_352701, BC047240 in example below

• NCBI_BLAST_example.htm: edited blast result - not possible to save exact NCBI display

Utilities

An XScufl model to test retrieving sequence using seqret and trimming.

• emblAccNumberAC099731seqret.xml: test seqret

-- MarkGreenwood - 05 Nov 2003

---

• emblAccNumberXLRHODOPseqretBlastn.xml: blastn_ncbi example
• emblAccNumberX07024seqretBlastn.xml:
• sequenceBlastn.xml:

• SequsaToBlastnEmbl.xml: test blastn workflow

• BlastNagainstDDBJatDDBJ.xml: blastn at DDBJ test