Percent identity vs. score

[cmp171]

https://github.com/brouwern/compbio2021/blob/4fc22d26cd66119a177fd9572bd409ffa989216d/KEY-MSA-walkthrough-shroom.Rmd#L391 When we calculate the percent identity of an alignment of 2 sequences ourselves, should we take the indels into account? There were a few questions on the practice exam where there are indels and those are included as differences in the correct calculation of percent identity.

[brouwern]

Which questions were there? Intel’s don’t normally count. There was a question with tricky layout where dots represented the same nucleotide as a reference sequence and it’s easy to think that they were supposed to indelz.

On Mon, Oct 4, 2021 at 4:44 PM cmp171 @.***> wrote:

https://github.com/brouwern/compbio2021/blob/4fc22d26cd66119a177fd9572bd409ffa989216d/KEY-MSA-walkthrough-shroom.Rmd#L391 When we calculate the percent identity of an alignment of 2 sequences ourselves, should we take the indels into account? There were a few questions on the practice exam where there are indels and those are included as differences in the correct calculation of percent identity.

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[cmp171]

Oh, yes that is the question that I was referring to. I accidentally read the dots as indels rather than as homologous to another sequence so I was confused about the PID calculation. Thank you!