User: Good Gravy

gravatar for Good Gravy
Good Gravy20
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20
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New User
Location:
United Kingdom
Last seen:
1 year, 11 months ago
Joined:
5 years, 6 months ago
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Posts by Good Gravy

<prev • 14 results • page 1 of 2 • next >
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What is a "good" HADDOCK score?
... [I am using the HADDOCK docking server](http://haddock.science.uu.nl). I am attempting to dock a protein to some dsDNA. All the energy values stack up, but I'm having trouble interpreting the more specific scores. My HADDOCK score is -90±2, the cluster size is 126. Are these within the "normal" rang ...
web-server protein-binding docking biophysics written 3.1 years ago by Good Gravy20
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Comment: C: Feature type locations overlap in Biopython. Which number is correct?
... Very informative, thanks. If I have understood you correctly, the only time this needs to be taken into account is when making the location integer into a  human readable position, and is not a worry for the amino acids sequence? For example would there be an amino acid that would be incorrectly pri ...
written 4.2 years ago by Good Gravy20
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Feature type locations overlap in Biopython. Which number is correct?
... In biopython feature.location.end can be equal to next_feature.location.start. For example:   type: TRANSMEM location: [187:208] qualifiers:     Key: description, Value: Helical. {ECO:0000255}.   type: TOPO_DOM location: [208:411] qualifiers:     Key: description, Value: Extracellular. {EC ...
python biopython written 4.2 years ago by Good Gravy20 • updated 4.2 years ago by Peter5.8k
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How to find transmembrane domain topological direction (extracellular/intracellular) from a uniprot text file?
... I am trying to sort the fasta sequence of residues in transmembrane domains from left to right by extracellular to intracellular residues rather than N terminal to C terminal. Currently I am isolating the domains using a similar biopython script to this post.  Originally I was writing a script that ...
sequence biopython uniprot written 4.3 years ago by Good Gravy20 • updated 4.3 years ago by Peter5.8k
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Comment: C: What kind of accession code is NP_000123.1?
... Super helpful, thanks! ...
written 4.4 years ago by Good Gravy20
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What kind of accession code is NP_000123.1?
... I am batch retrieving a few hundred codes that vary slightly in length and sometimes have XP rather than NP. In uniprot, from the dropdown selection (see below image) in the batch retrieval page, what database should I convert from?   ...
database written 4.4 years ago by Good Gravy20 • updated 4.4 years ago by lelle800
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Comment: C: How to download UniProt files using Python and XML
... Will do, thanks for the help! ...
written 4.6 years ago by Good Gravy20
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Comment: C: How to download UniProt files using Python and XML
... I have a perl script that can parse the TM domain out. But for technical reasons I want to be able to get the TM domains directly from uniprot. The answers mentioned in the question show this is possible in both biopython and java, I am looking for a way to do this in python alone. ...
written 4.6 years ago by Good Gravy20
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Comment: C: How to download UniProt files using Python and XML
... The problem still remains how to only get the TM domain. This method does indeed fetch the fasta sequences, but of the entire protein. ...
written 4.6 years ago by Good Gravy20
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How to download UniProt files using Python and XML
... This question follows from another question - question that asks about how to retrieve transmembrane (TM) domains from uniprot. The top answer in that question mentions that the UniProt XML format can be used to retrieve a fasta sequence of each TM region.   filenames = ["O43561.xml", "P08195.xm ...
python uniprot written 4.6 years ago by Good Gravy20 • updated 4.6 years ago by Bioinformatics_NewComer320

Latest awards to Good Gravy

Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to download UniProt files using Python and XML
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Are there any specialist transmembrane protein databases?

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