Bioinformatics Methods for DNA Motif Finding and PSSM

1

Bioinformatics Methods for DNA Motif Finding and PSSM

The chart below is a position specific scoring matrix (PSSM

Bioinformatics assignment: motif finding and transcription factor binding site prediction

Name____________________________________

The chart below is a position specific scoring matrix (PSSM, a logarithmic transformed matrix) for a transcription factor binding site. (1). Evaluate a sequence “GACATTCA” to find out which segment of the sequence fits the binding site best. (2) What is the max score that a sequence can have with this PSSM? (3) What is the minimum score a sequence can have with this PSSM?

There are many programs for transcription binding site prediction available free on the internet. Find a few of them, list the links to at least 2 websites. Test with the following sequence to see how it…