[BioPython] Seq utilities

[Jeffrey Chang]

Sounds like something we can put in /Scripts.  Let me know how it goes!

Jeff


On Fri, 28 Apr 2000, Cayte wrote:

>    I think the translate utilities need a pick list.  If you want, I can take a crack at a simple TK menu.  
> It doesn't need to be elaborate.
> 
> USER STORY:    Peter Mold works for a pharmaceutical company that makes antibiotics.  He is writing a short script to translate  a piece of mold DNA.  He wonders, "Do  I want Mold Mitochondria" or Mitochondrial Mold? Was mold captialized?."  He needs to code inspect to find the anwer, but he doesn't remember whether the code was in IUPAC.py or in Codon.py or which directory to search.
> 
>    Also, I think the translation from protein to DNA needs several options.
> 
>         To present a list of possible candidate DNA sequences.
> 
>          To sort the candidate sequences on the basis of probability.
> 
>          Probability distributions based on the type of organism.
> 
> USER STORY:       Mary Rainforest has found an interesting protein in an orchid.  She would like to find the DNA sequence and find if similar plants have a similar sequence.  She would like to find the sequence that is correct for this plant and doesn't think if is the default back translation.  She decides to mark the ambiguous codons with a felt tip pen and do the lookups herself.
> 
> 
>                                                                                    Cayte
> 
>                                  
> 
> 
>         
>