Sequences

The Sequence object provides generic biological sequence manipulation functions, plus functions that are critical for the evolve module calculations.

Generic molecular types

Sequence properties are affected by the moltype you specify. The default type for a sequence is "text".

In some circumstances you can also have a "bytes" moltype, which I’ll explicitly construct here.

DNA and RNA sequences

Creating a DNA sequence from a string

Sequence properties are affected by the moltype you specify. Here we specify the DNA MolType.

Creating a RNA sequence from a string

Converting to FASTA format

Convert a RNA sequence to FASTA format

Creating a named sequence

You can also use a convenience make_seq() function, providing the moltype as a string.

Setting or changing the name of a sequence

Complementing a DNA sequence

Reverse complementing a DNA sequence

Translate a DnaSequence to protein

Converting a DNA sequence to RNA

Convert an RNA sequence to DNA

Testing complementarity

Joining two DNA sequences

Slicing DNA sequences

Getting 3rd positions from codons

The easiest approach is to work off the cogent3 ArrayAlignment object.

Getting 1st and 2nd positions from codons

In this instance we can use features.

Return a randomized version of the sequence

Remove gaps from a sequence