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Bioinformatics Part II

Updated on December 29, 2012

As promised!

Here's the next part of my talk from this summer, in the form of powerpoint slides with commentary:

This is the central dogma in biology.
This is the central dogma in biology.

According to Tomkins, a major problem with nearly all past human-chimp comparative DNA studies is that data often goes through several levels of pre-screening, filtering and selection before being aligned, summarized, and discussed. Non-alignable regions are typically omitted and gaps in alignments are often discarded.

This is an informational talk, I will draw not conclusions about the strength of the data.
This is an informational talk, I will draw not conclusions about the strength of the data.
I chose this gene because it’s conserved among organisms with a complex eye, so we expect the sequences to be similar.
I chose this gene because it’s conserved among organisms with a complex eye, so we expect the sequences to be similar.
How many of you have used Entrez?
How many of you have used Entrez?

Check out Entrez's help page for a description of the service.

Entrez offers a really neat tool! Take a look at the BLAST homepage, and click on "more" to see a description.

BLAST is most useful at the protein level, since there are changes at the nucleotide level that aren’t reflected in the protein.  (Intron splicing, single nucleotide polymorphisms, etc.) FASTA is a text-based representation of nucleotides/peptides.
BLAST is most useful at the protein level, since there are changes at the nucleotide level that aren’t reflected in the protein. (Intron splicing, single nucleotide polymorphisms, etc.) FASTA is a text-based representation of nucleotides/peptides.

Here we've aligned the human and chimpanzee versions of the PAX3 gene. The image above represents the screen that appears when the BLAST tool is done. The two sequences have 100% identity, meaning that they align perfectly.

Watch for the next post, in which I will demonstrate another database, called Genome Browser. We'll go back over BLAST as well.

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