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Structural Biochemistry and Bioinformatics

Sequence alignment and databases

Today we are going to learn how to use sequence alignment tools. The tools we are going to use are fasta, blast, blastpgp and ssearch.

Assignments on local machines

You should use this sequence and search a database that contains a representative set of the sequence of all known protein structures. The proteins have a 4 number code at the end so that you know if they have a similar structure or not. First you should learn how to use blast, fasta, and ssearch then you should answer the following questions.

Assignments on the web

Many searches can be done using the WWW. Below you will use some available servers. To search and align proteins. These are the three assignment you should do.

1. NCSA Biology Workbench
2. Blast and Fasta
3. Alignments