Open a BLAST database file using a similarity search

*Note: If you intend to use the enhanced functionality of SeqBuilder Pro for sequence analysis, you should import the online database sequences there. This saves several steps compared to opening them in GeneQuest and then exporting them to SeqBuilder Pro. The search and import functionality is identical in both applications.

To perform a BLAST search:

1. Select the sequence or portion of sequence that you want to search for.

2. Choose Net Search > BLAST Selection or Net Search > BLAST ORF.
   
   
   
   
   • The Server field lists the currently selected BLAST server. You may change to a different server by choosing one from the drop-down list provided, or choose A New Server and then type a new URL.
     
     
   • The Programs field lists the currently selected BLAST program. The following programs are available through this list, though some servers may not offer all of these programs:
     
     
     • blastn searches a nucleotide sequence database with a nucleotide query sequence.
       
     • blastp searches a protein sequence database with an amino acid query sequence.
       
     • blastx searches a protein sequence database with the six-frame translation of a nucleotide query sequence.
       
     • tblastn searches the six-frame translation of a nucleotide sequence database with a protein query sequence.
       
     • tblastx searches the six-frame translation of a nucleotide sequence database with the six-frame translation of a nucleotide query sequence.
       
       
   • The Database field lists the database that will be searched. Choose from the databases available on the server by selecting one from the list provided. Using less common databases may cause a noticeably slower search. According to NCBI, this is because the less frequently used databases may not already be loaded in memory on an available server. In contrast, frequently used databases such as nr or nt are already loaded in memory on a number of servers. Also note that available databases may include the refseq_representative_genomes database. This database contains representative bacterial/archaeal genomes, as opposed to all the genomes (some of which are multiples) now in Genbank or RefSeq. The refseq_representative_genomes database can be helpful when matches to Escherichia coli/Shigella, for example, occupy all 100 of the top BLAST results. For example, say you want to find the location of a particular sequence in the curated "model organism version" of the E. coli K-12 MG1655 genome (U00096.3/NC_000913.3). Here is the location of the true sequence match when using different databases: refseq_genomic - absent from top 100 hits. nr - far down the list of the top 100 hits. refseq_representative_genomes – the top hit.

3. After confirming the values in the Query dialog, click OK to initiate the search. Once the search is completed, any matches are displayed in the BLAST Search Results window. You may continue to work with other Lasergene application activities while waiting for BLAST search results, but you cannot launch another BLAST search until you close the current BLAST window.