ICM provides a fast tool to search any Blast-formatted database with a query sequence
and generate an alignment on the fly. For example you can use this option to find template structures for homology modeling.
- Select Bioinfo/Search and Align (or right click on a sequence)
- Enter the sequence name you wish to search against the database with.
- Locate the blast-formatted database to search. You can download Blast formatted databases from here ftp://ftp.ncbi.nih.gov/blast/db/ eg. pdbaa - PDB sequence database.
- Specify the speed parameter (0 is the slowest, but the most detailed, 100 is the fastest search for nearly identical sequences).
- Enter the number of hits you would like to view
- Enter an identity threshold filter to narrow down the number of hits.
- The top hits will be displayed in a table.