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 molecular type.

Creating a RNA sequence from a string

Converting to FASTA format

Convert a RNA sequence to FASTA format

Writing a sequence to file

Creating a named sequence

Setting or changing the name of a sequence

Complementing a DNA sequence

Reverse complementing a DNA sequence

Translate a sequence to protein

The default is to trim a terminating stop if it exists. If you set trim_stop=False and there is a terminating stop, an AlphabetError is raised.

You can also specify the genetic code.

Translating a DNA sequence containing stop codons

By default, get_translation() will fail if there are any stop codons in frame in the sequence. You can allow translation in these cases by setting the optional argument include_stop=True.

Converting a DNA sequence to RNA

Convert an RNA sequence to DNA

Testing complementarity

Joining two DNA sequences

Getting all k-mers from a sequence

Note

By default, any k-mer that contains an ambiguity code is excluded from the output.

You can include ALL k-mers by setting strict=False.

Slicing DNA sequences

Obtaining the codons from a DnaSequence object

Use the method get_in_motif_size

Getting 3rd positions from codons

Getting 1st and 2nd positions from codons

In this instance we can use features.

Return a randomised version of the sequence

Remove gaps from a sequence

Getting GC% by counting states

We can obtain the percentage of GC nucleotides by using the counts method on sequences. This returns an object that behaves like a dictionary.

Note

Other arguments on the counts() method allow including ambiguous or gap characters in the result.

Counting k-mers

A k-mer is a word of size \(k\) and, as is the convention, its counts are derived from all possible positions (as distinct from non-overlapping words which is how motif counts are calculated).

In this case, the result is a numpy array with the order of elements corresponding to the result of

Note

We support third-party plugins for k-mer counting. After installing one, they can be selected by specifying the package with the .count_kmers(k=2, use_hook="<package name>").