Flounder
Tools to score a DNA sequence using the Flounder method.
codon_score(sequence)
Return the codon-based Flounder Score for the given sequence.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
The sequence to score. |
required |
Returns:
| Type | Description |
|---|---|
int
|
The score for the sequence. |
This scoring system translates the codons in the sequence into AA codes, and then builds a score based on them. Translation of the sequence always starts with the first base, and keeps going as long as there are codons left. Stop codons are scored as 0 and worked past.
codon_scores(sequence)
Return a list of codon-based Flounder Scores for the given sequence.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
The sequence to score. |
required |
Returns:
| Type | Description |
|---|---|
list[tuple[str, int]]
|
A list of tuples, the codon and its score. |
This scoring system translates the codons in the sequence into AA codes, and then builds a score based on them. Translation of the sequence always starts with the first base, and keeps going as long as there are codons left. Stop codons are scored as 0 and worked past.
score(sequence)
score_to_the_max(sequence)
Return the to-the-max Flounder Score for the given sequence.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
The sequence to score. |
required |
Returns:
| Type | Description |
|---|---|
int
|
The flounder score for the sequence. |
The to-the-max flounder score is like the flounder score, but other than scoring the individual base, it scores based on the base and also every IUAPC code that applies.
scores(sequence)
scores_to_the_max(sequence)