Harvard:Biophysics 101/2007/Notebook:Katie Fifer/2007-4-24: Difference between revisions
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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...) |
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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. | ||
----- for example ----- | |||
<pre> | |||
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 | |||
</pre> | |||
is something we want to get back and then be able to parse through | |||
Latest revision as of 00:02, 24 April 2007
- 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
