The identical() function fails in Biostrings as can easily be seen from:

> temp1 <- DNAString('AAA')
> temp2 <- DNAString('AGA')
> identical(temp1, temp2)
[1] TRUE

It seems like it only looks at the length:

> temp3 <- DNAString('AGAG')
> identical(temp1, temp3)
[1] FALSE

But the == function works:

> temp1 == temp2
[1] FALSE

Hi Kristoffer,

Please see Comparing AAStrings using identical() instead of == for an answer to this.

Cheers,

H.