How did they find these position specific scoring matrix scores?
1
0
Entering edit mode
16 months ago
jbrody11 • 0

My lecture notes in Bioinformatics try to explain how to work out position specific scoring matrix, or position weight matrix. They use the following example in the notes. I understand the formula but I don't see how they could calculate -2.94 for a frequency/base count of 0, as log2(0) isn't a number. Could somebody explain how they might have found -2.94 for the 0 base counts? I am also not sure what pb value they used. I assume fbi means the base count (frequency) Image here of their explanation

sequence alignment sequencing • 318 views
ADD COMMENT
1
Entering edit mode
16 months ago
Mensur Dlakic ★ 12k

Zero counts in sequence alignments is a common occurrence for biological sequences. Small pseudocounts are added to avoid numerical issues - see here. In practical terms this means that each residue will have a non-zero frequency.

ADD COMMENT

Login before adding your answer.

Traffic: 1263 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6