Lab 15 - Bioinformatics

Today we had a very quick and shallow introduction to the field of bioinformatics.

We took a quick tour through the NCBI website, home of GenBank (a database) and BLAST (an algorithm to do sequence pairwise alignments). We started with some problem sequences and we found out what organism they came from and what DNA fragment they corresponded to.

We also introduced the Fasta file format and put together a file to do a multiple sequence alignment using ClustalW.

Remember, this was a very shallow introduction to bioinformatics. There are many more possibilities and applications that you will explore on your own, or as part of research projects when getting a job or attending grad school.

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Links for Bioinformatics lab

The following links will provide fast access to the web pages you need to do your bionformatic exercises:

• National Center for Biotechnology Information (NCBI)
• DNA Data Bank of Japan (DDBJ)
  
• European Bioinformatics Institute (EBI)

• GenBank statistics
• Clustal W
• Phylogeny software
  

• NCBI's Coffee Break

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Lab 03 - PCR of the PV92 Alu insertion locus (gel electrophoresis)Lab 14 - Size exclusion chromatography (SEC)

Today we ran a gel to confirm the results of the PCR in which the target was the PV92 Alu insertion locus in our own DNA. Results will be published soon...

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Students also did lab 14, size exclusion chromatography (SEC). It is the second kind of chromatography that we have performed (the first one was hydrophobic interaction chromatography HIC)).

The kit provided a mix of hemoglobin and Vitamin B12, proteins that have very different sizes and can be easily separated using the featured technique.

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Lecture, chapter 11 - Regulation of gene expression at the RNA level

Today we finished chapter 11 on regulation of gene expression at the RNA level.

We talked about how cells have incorporated RNAi as another tool to control gene expression. We also talked about some particularities of RNA, used for control of gene expression, like riboswitches.

Next week: The main highlights of RNA processing and molecular techniques.

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Lecture, chapter 11 - Regulation of gene expression at the RNA level

Today we covered most of chapter 11, on regulation of gene expression at the RNA level.

We talked about the different ways in which an mRNA transcript may be manipulated or modified as to stop, slow, or enhance its translation. The last topic we covered was RNA interference (RNAi).

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