Practical Work: Database search with Blast

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.

During this practical please use either EMBnet's basic blastor advanced blast pages.

Reminder: some links for the recovery of sequences

[ Easily fetch sequences ][ Search SWISS-PROT ][ NCBI's Entrez ]

Database search with Blastp

Use the protein sequence CC16_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:

Database search with Blastx

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:

Supplementary exercise

Take a look at the database choice available on the advanced blast page. More information about the databases is available on thedatabase help page.

Questions and comments can be sent to Volker Flegel