Sequence Searching of the Vector NTI Database

A BLAST search of your various Molecule Databases cannot be performed easily, but one can perform a search of these Databases that is similar to the Motif Search function of Vector NTI. This can be used to search either the DNA/RNA Molecule or Protein Database. The user can choose to search the entire database or a specific subset. In a DNA sequence search, both strands of all molecules in the database will be searched.

Searching the DNA/RNA Molecule database.

Choose a sequence you wish to search for and use the New > Oligo function in your Oligo database to create this sequence as a new oligonucleotide. The sequence you wish to search for should be present in your Oligo Database if you want to save it or redo the search at a later date.

Display your DNA/RNA Molecule Database and choose Database > Search from the list of drop down menus.

In the new window check the Oligo and Peptide Filter option and open up the “Oligo and Peptides setup”. In the new window choose the “Add Oligos” tab and then the “Oligo Database…” option to search for your sequence of interest in the Oligo Database and select it. Select OK and get back to the window below.

At this point you can change any of the three parameters highlighted with arrows to suit your search. Then choose “OK” to get back to the Molecule Database Search window. You can choose to search the DNA/RNA Main database or select a specific subset within to search. Choose “Start Search” and if the search is successful, the following window will appear. Choose a name for the subset and all the molecules in the database matching your search criteria will appear in a new subset.

The longest sequence we have tested using this search function is the ampicillin resistance gene of pUC19 (858 bp).

Searching the Protein Molecule Database.

This function will generally follow the same outline as above except that you do not create the string of amino acids you wish to search for in the Oligo Database, but simply type or paste the string you wish to search for in the Oligo and Peptide Setup window using the “Add Peptide” function and then select the entire Protein Database or a specific subset to be searched.