[BioPython] Seq utilities

Cayte katel@worldpath.net
Fri, 28 Apr 2000 18:54:12 -0700


This is a multi-part message in MIME format.

------=_NextPart_000_0040_01BFB143.24C3CC40
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

   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

------=_NextPart_000_0040_01BFB143.24C3CC40
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2314.1000" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>&nbsp;&nbsp; I think the translate utilities need a =
pick=20
list.&nbsp; If you want, I can take a crack at a simple TK menu.&nbsp;=20
</FONT></DIV>
<DIV><FONT size=3D2>It doesn't need to be elaborate.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>USER STORY:&nbsp;&nbsp;&nbsp;&nbsp;Peter Mold works =
for a=20
pharmaceutical company that makes antibiotics.&nbsp; He is writing a =
short=20
script to translate  a piece of mold DNA.&nbsp; He wonders, =
"Do&nbsp;&nbsp;I=20
want Mold Mitochondria" or Mitochondrial Mold? Was mold =
captialized?."&nbsp; 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>&nbsp;</DIV>
<DIV><FONT size=3D2>&nbsp;&nbsp; Also, I think the translation from =
protein to DNA=20
needs several options.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; To =
present a list=20
of possible candidate DNA sequences.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; To =
sort the=20
candidate sequences on the basis of probability.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
Probability=20
distributions based on the type of organism.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>USER STORY:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mary =

Rainforest has found an interesting protein in an orchid.&nbsp; She =
would like=20
to find the DNA sequence and find if similar plants have a similar=20
sequence.&nbsp; She would like to find the sequence that is correct for =
this=20
plant and doesn't think if is the default back translation.&nbsp; She =
decides to=20
mark the ambiguous codons with a felt tip pen and do the lookups=20
herself.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT=20
size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
Cayte</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT=20
size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
</FONT></DIV></BODY></HTML>

------=_NextPart_000_0040_01BFB143.24C3CC40--