[BioPython] Seq utilities
Cayte
katel@worldpath.net
Fri, 28 Apr 2000 18:54:12 -0700
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I think the translate utilities need a pick list. If you want, I can =
take a crack at a simple TK menu. =20
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
=20
=20
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<DIV><FONT size=3D2> I think the translate utilities need a =
pick=20
list. If you want, I can take a crack at a simple TK menu. =20
</FONT></DIV>
<DIV><FONT size=3D2>It doesn't need to be elaborate.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2>USER STORY: Peter Mold works =
for a=20
pharmaceutical company that makes antibiotics. He is writing a =
short=20
script to translate a piece of mold DNA. He wonders, =
"Do I=20
want Mold Mitochondria" or Mitochondrial Mold? Was mold =
captialized?." He=20
needs to code inspect to find the anwer, but he doesn't remember whether =
the=20
code was in IUPAC.py or in Codon.py or which directory to =
search.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2> Also, I think the translation from =
protein to DNA=20
needs several options.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2> To =
present a list=20
of possible candidate DNA sequences.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2> To =
sort the=20
candidate sequences on the basis of probability.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2> =
Probability=20
distributions based on the type of organism.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2>USER STORY: Mary =
Rainforest has found an interesting protein in an orchid. She =
would like=20
to find the DNA sequence and find if similar plants have a similar=20
sequence. She would like to find the sequence that is correct for =
this=20
plant and doesn't think if is the default back translation. She =
decides to=20
mark the ambiguous codons with a felt tip pen and do the lookups=20
herself.</FONT></DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><FONT=20
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Cayte</FONT></DIV>
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<DIV><FONT=20
size=3D2> &nbs=
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<DIV> </DIV>
<DIV><FONT size=3D2> =20
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