LAB - Bioinformatics

DNA sequence alignment viewed with the multiple alignment editor Se-Al. On the far right there are insertions and/or deletions in several sequences (click pic for full-size image)

We had laptops for each student in the lab and had a small and crude (quick and dirty?) overview of some of the few tools available in bioinformatics.

The main focus of our exercise was the use of the algorithm known as BLAST (Basic Local Alignment Search Tool), available at the NCBI webpage. After an overview of some of the main features of the site (which is updated VERY frequently), we "BLASTed" (used BLAST) a few unknown protein (using 'protein BLAST') and nucleotide (using 'nucleotide BLAST') sequences. We found out what the sequences were and to what organisms they belonged. This is one of many possible uses of the BLAST algorithm.

During this lab students were also introduced to the fasta file format and its use for sequence alignment. After finding out what our problem nucleic acid sequences were (by BLASTing)and to what organisms they belonged we made a fasta file with all of them and aligned them using an on-line version of ClustalW available on the European Bioinformatics Institute website.

The following learning outcomes should have been met:

• Introduction to the concept and field of bioinformatics
• Introduction to the main sequence data repository in the Americas and one of the main in the world: NCBI
• Introduction to the main database in the NCBI website: GenBank
• Basic understanding of the fasta file format
• Basic use of the BLAST algorithm
• Introduction to the concept of sequence alignment

Lab report

The lab report can be typed and it won't follow the format of the previous reports. Please include:

• An brief introduction explaining what bioinformatics is
• A summary of the exercises performed in the lab (methods)
  
• Findings about the problem sequences. What organisms did they belong to? What proteins and genes were they? - Include the three first hits for each search if available. No need to include the actual sequences
• Research question: What are the potential uses of a sequence alignment?

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