Questions tagged [python]
python is a programming language, widely used in bioinformatics
620
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Introducing a fixed number of random substitutions in a sequence
I'm writing a function that introduces $n$ substitutions inside a sequence of nucleotides.
I have a working version, but I'm looking for any other ways of doing this:
...
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Facing problem with BLASTx using BioPython in Google Colab
I'm trying to BLASTX a sequence using Biopython in Google Colab. Here is the code I am using. I'm not able to understand why I am getting an empty list [] for ...
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opensource PyMOL compiling-install issue
Hi I am playing a little bit with schrodinger /
pymol-open-source
Trying to figure out how : python setup.py install works I found documentation in
pymol-open-...
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How can I visualize protein secondary structure?
I'm currently working on a secondary structure prediction model and I'd like to visualize what will be predicted , the format of secondary structure sequence is consisted of 8 labels:
G: 3-turn helix ...
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1
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Waterman-Smith-Beyer implementation in Python
I am working on a text aligner to help me get a better understanding of specific steps necessary to perform sequence alignment. So far, things have been going great but I noticed yesterday that my ...
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LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. ...
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Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank
Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank(https://www.rcsb.org/).
Or is there a way to extract the data programaticaly ...
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1
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Fixation index calculation from the vcf files
I used the Python script FSTest (https://github.com/similab/FSTest) for the calculation of the fixation index from the extracted SNPs. I used the following command:
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2
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Python/R/bash script to ease the comparison of different protein complexes in PDB
I would like to create a table of comparison among similar protein complexes from the pdb.
This would be based on their numbers of proteins and the presence of each protein.
Is there any way like ...
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2
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Multi-pattern search in aligned sequences
I am currently working on a bioinformatics problem where I need to lookup and count the location and count of occurences of 4000-ish 5 character long patterns in each sequence of a fasta file of 700GB....
3
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2
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Running multiple sequence using spades.py on an HPC
I am trying to run a batch script to assemble sequences using the spades.py command on HPC. I tested the script with one sequence (1 forward and 1 reverse read) and this worked. I have 100 sequences ...
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Biopython / ETE3 get subtree of a newick tree
I can not find a good example how to extract a subtree from a phylogenetic tree with either library.
I can load newick files etc, but not sure how to search for a ...
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Using Python for Monte Carlo simulation for predicting protein nucleation aggregation
I want to write a code for a Monte Carlo simulation to determine the maximum stable complexes in a protein nucleation reaction. Also, need to graph the results for the same.
Here is the problem ...
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Does PGS Catalog limit the number of queries to their FTP server?
I am calculating a polygenic risk score (PGS) from the PGS Catalog using the following command:
...
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Trying to plot the results of GSEA in python
I'm having some major chaos with the output table generated and then passing that to my plot function. New to this (1st time), could somebody review this piece of code and suggest some corrections. I ...
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