Harvard:Biophysics 101/2007/Notebook:Katie Fifer/2007-4-24

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(New page: * we're going to pull the genbank file down in its entirety and parse for relavant features using the code i wrote last time. (we gave up the battle to get just a piece of the genbank file...)
Current revision (02:02, 24 April 2007) (view source)
 
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* we're going to pull the genbank file down in its entirety and parse for relavant features using the code i wrote last time. (we gave up the battle to get just a piece of the genbank file for now... someday hopefully someone will come up with a better way of doing this but we're just trying to move forward for now.....)
* we're going to pull the genbank file down in its entirety and parse for relavant features using the code i wrote last time. (we gave up the battle to get just a piece of the genbank file for now... someday hopefully someone will come up with a better way of doing this but we're just trying to move forward for now.....)
* NCBI gene, for each gene that we get back, has files about each gene containing literature sources and info about exons/introns etc... I'm going to work on parsing this for tomorrow and thursday.
* NCBI gene, for each gene that we get back, has files about each gene containing literature sources and info about exons/introns etc... I'm going to work on parsing this for tomorrow and thursday.
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----- for example -----
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<pre>
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CFTR Links
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Official Symbol: CFTR and Name: cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) [Homo sapiens]
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Other Aliases: tcag7.78, ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR, dJ760C5.1
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Other Designations: cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7); cystic fibrosis transmembrane conductance regulator/ATP-binding cassette sub-family C member 7
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Chromosome: 7; Location: 7q31.2
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MIM: 602421
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GeneID: 1080
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</pre>
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is something we want to get back and then be able to parse through

Current revision

  • we're going to pull the genbank file down in its entirety and parse for relavant features using the code i wrote last time. (we gave up the battle to get just a piece of the genbank file for now... someday hopefully someone will come up with a better way of doing this but we're just trying to move forward for now.....)
  • NCBI gene, for each gene that we get back, has files about each gene containing literature sources and info about exons/introns etc... I'm going to work on parsing this for tomorrow and thursday.

for example -----

 CFTR	 Links
Official Symbol: CFTR and Name: cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) [Homo sapiens]
Other Aliases: tcag7.78, ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR, dJ760C5.1
Other Designations: cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7); cystic fibrosis transmembrane conductance regulator/ATP-binding cassette sub-family C member 7
Chromosome: 7; Location: 7q31.2
MIM: 602421
GeneID: 1080

is something we want to get back and then be able to parse through

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