The following examples are for using the computing facilities via direct login to an appropriate AMDeC UNIX host computer. Easy-to-use web interfaces to the BlastMachine and GeneMatcher2 are also available.

In the following example, input_file contains your query sequence, and output file is the file to which you would like the search result stored.

BlastMachine

The BlastMachine is run through a client program, pb, available on all of the login hosts. It uses standard NCBI blastall commands.

To run a blastn search against the current copy of the NCBI 'nt' database (non-redundant nucleotide):

pb blastall -p blastn -d ncbi/nt -i input_file -o output_file

To run a blastp search against the current copy of the NCBI 'nr' database (non-redundant protein):

pb blastall -p blastp -d ncbi/nr -i input_file -o output_file

See Databases for a full list of sequence databases available for search. (Note that NCBI on their Blast search pages refer to both of the above databases as 'nr').

pb blastall accepts all standard NCBI blastall arguments.

GeneMatcher2

1. To run a Smith-Waterman search of a nucleotide query sequence against the current copy of the NCBI 'nt' (non-redundant nucleotide) database:

btk search swn dbset=nt query=input_file matrix=dna.mat output=output_file

(this can be abbreviated as 'btk swn ......', omitting 'search' ).

 

2. To run a Smith-Waterman search of a protein query sequence against the current copy of the NCBI 'nr' (non-redundant protein) database, using the blosum62 scoring matrix:

btk swp dbset=nr query=input_file matrix=blosum62 output=output_file

 

3. Imagine you have run a search using the GeneMatcher2 web interface (Bioview Workbench) which you expect has produced an enormous output file, one too large to view in the web browser. You can use these steps to retrieve the results:
   
   
   1. The search results are stored on the GeneMatcher2 as a post-processing set (ppset). View a list of the ppsets by typing the command:
      
      btk ppset list
      
      
   2. Find the ppset of interest and note its ID number. You can now retrieve this ppset using the command:
      
      btk ppset output id=id output=output_file
      
      There are additional output options that can be view by issuing the command:
      
      btk ppset output -help
      

4. Note about Matrices:

The easiest way to examine the various scoring matrices available on the GeneMatcher2 is via the Bioview Workbench web interface.

 

BLAST on the UNIX hosts.

NCBI blastall is available on the Beowulf Cluster, where it can be run in a multithreaded mode. See the Cluster page for further details.

We do not recommend routine use of the local BLAST on the UNIX login hosts, especially for any large jobs. However there may be cases, e.g. comparisons of small sequences as part of some larger scripted process, where it might be appropriate.

To run a blastn search against the current copy of the NCBI 'nt' database:

blastall -p blastn -d ncbi/nt -i input_file -o output_file

 

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