If, on the USCS Genome Bioinformatics home page here, you click on BLAT and then look down to the info at the bottom of the page, you will find an explanation of how the software works. I had been confused by the terms 11-mer (for searching DNA) and 3-mer (for searching proteins). These refer to the number of subunits, so the BLAT indexes non-overlapping segments of DNA of 11 bases in length, and non-overlapping segments of proteins of 3 amino acids length. These indices are searched when we try to match a DNA or protein sequence to an existing genome (proteome).
I am still working my way through the guided example, and have not yet tackled the two unguided ones that follow in the downloadable Hands-on Exercises pdf found here. On my first try at the guided exercise, the screen I got did not exactly match the tutorial's, and I want to figure out why. I am still trying to decide exactly how far I want you to go on this, and what you will turn in for credit. I will let you know the moment I do. In the meantime, email with any questions you have-- (No--strike that: I have questions and confusions of my own!) Email me as soon as you get stuck: that is, unable to figure out what to do next, totally lost. My email is jmichalsbr@aol.com
I am still working my way through the guided example, and have not yet tackled the two unguided ones that follow in the downloadable Hands-on Exercises pdf found here. On my first try at the guided exercise, the screen I got did not exactly match the tutorial's, and I want to figure out why. I am still trying to decide exactly how far I want you to go on this, and what you will turn in for credit. I will let you know the moment I do. In the meantime, email with any questions you have-- (No--strike that: I have questions and confusions of my own!) Email me as soon as you get stuck: that is, unable to figure out what to do next, totally lost. My email is jmichalsbr@aol.com
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