The following exercises will introduce you to the principle of database searches using the blast tools.
These tools allow the biologist to find sequences similar to his query sequence. They are routinely used to identify homologuesof proteins, distantly related sequences, functional domains, etc.
Many web-based blast-services are available to the biologist. They differ in the structure of the web-interface, the amountof parameters that can be modified and the number of different databases. The frequency with which the databases are updated to reflectthe latest changes, may also vary between servers.
|NCBI BLAST Server||Very well maintained blast server located at the NCBI; where the blast tools are developped.|
During this practical please use either EMBnet's basic blast or advanced blast pages.
Reminder: some links for the recovery of sequences
[ Search SWISS-PROT ][ NCBI's Entrez ]
Use the protein sequence CDC16_SCHPO as query to search for similar sequences in theSwiss-Prot database, using the program blastp. Use the default parameters andtry to answer the following questions:
The EMBL W99073 sequence is a mouse EST. Compare this nucleotide sequence to the Swiss-Protdatabase using the blastx program on the basic blast page.
Try to answer the following questions:
Take a look at the database choice available on the advanced blast page. More information about the databases is available on the database help page.