Dan
  • Member for 4 years, 5 months
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1 answers
4 votes
74 views
What does the "X_OS_IND" column mean?
5 votes

According to this link, 1=death 0=censor and null=no data.

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2 answers
7 votes
41 views
how to find the bound form of an enzyme structure?
5 votes

Tried looking for an explicit database? i.e. ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder: https://www.ncbi.nlm.nih....

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3 answers
9 votes
133 views
PDB format: remark number for free text
Accepted answer
4 votes

From this document, it looks like REMARK 250 is the way to go.

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2 answers
4 votes
478 views
How to dump genes from GenBank in GFF3 format?
Accepted answer
3 votes

Turns out you can just grab the GFF3 from the NCBI's FTP site! ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/195/GCA_000003195.3_Sorghum_bicolor_NCBIv3/ See: https://www.ncbi.nlm.nih.gov/...

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2 answers
8 votes
105 views
How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?
2 votes

No, this doesn't makes sense (I think). The hydrophobicity of an AA is the hydrophobicity of the AA, in whatever context, just like it's molecular weight. It's weight is it's weight, in a structure ...

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2 answers
4 votes
336 views
Reordering scaffolds according to a reference without a genetic map
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2 votes

I've been using ATAC to successfully align different versions of the rice genome assembly. There is a chance it will work for you between two closely related species (potato and tomato work well for ...

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2 answers
0 votes
102 views
How can I find the relevant pathway map from gene-gene or protein-protein interaction list?
2 votes

See a project like Plant reactome, where they infer the pathways of all sequenced plant genomes using orthology to well annotated species. http://plantreactome.gramene.org/

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4 answers
6 votes
2k views
Convert rs ID of one hg build to rs IDs of another build
1 votes

See also CrossMap: http://crossmap.sourceforge.net/ 20, 21, 22, 23, 24, 30

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3 answers
9 votes
3k views
How to convert GFF3 to GTF2
1 votes

The GenomeTools package has lots of small applications that let you massage GFF3. It may have a converter, or it may let you tweak your existing GFF3 so that gffread works

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3 answers
4 votes
537 views
Best distance parameter for estimating physical interaction between residues in a PDB file
1 votes

You should read my paper, where I did a comprehensive parameter sweep across different thresholds and definitions and benchmarked the resulting empirical potentials on a decoy ranking challenge: The ...

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1 answers
7 votes
136 views
What is a good pipeline for using public domain exomes as controls?
1 votes

I gather that you want to use the background SNP frequency as a prior for input to your SNP calling algorithm? I'm not sure of a canned algorithm for doing this, but a quick google shows up some ...

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3 answers
4 votes
537 views
Best distance parameter for estimating physical interaction between residues in a PDB file
Accepted answer
1 votes

Use a distance cutoff of 12Å between Cᵦ atoms.

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2 answers
3 votes
502 views
what is the difference between local identity and global identity for homolog finding?
1 votes

Defining homology isn't as simple as an identity cutoff, however, you're right that homology seems likely given a certain identity. This is where e-value comes into play. See: https://en.wikipedia.org/...

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5 answers
4 votes
3k views
using python to write bioinformatics pipelines tutorial
0 votes

Have a look at luigi for writing pipelines in python. You can found BioLuigi if you like :-P

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