Manipulating biological data¶
Sequences and Alignments¶
- Loading an alignment from a file or url
- Specifying the sequence molecular type
- Making an alignment from standard python objects
- Making a sequence collection from standard python objects
- Loading sequences using format parsers
- Sequence Collections and Alignments
Sequence- Protein sequences
- Annotations
- Annotations with coordinates
- Molecular types
- Alphabets
Genetic code¶
- Available genetic codes
- Translate DNA sequences
- Translate all six frames
- Find out how many stops in a frame
- Translate a codon
- Look up the amino acid corresponding to a single codon
- Get all the codons for one amino acid
- Get all the codons for a group of amino acids
- Converting the
CodonAlphabetto codon series - Obtaining the codons from a
DnaSequenceobject - Translating a DNA sequence with a terminating stop codon