Bioinformatics Stack Exchange
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How to install DnaSP on a Mac

I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data. However, its not working on my mac. I'm using wine to install it using these instructions for wine. Wine usually successfully…
Mollie Passacantando
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3 answers

Where can I find a database that has phenotype information together with associated SNPs?

I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association. Moreover, for some species, there are not even…
Haohan Wang
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Error installing VEP on mac

I have tried multiple different ways to get Ensemble's Variant Effect Predictor (VEP) to properly install on my mac, but I keep getting same error. In /Users/username/ensembl-vep/htslib make: Nothing to be done for `all'. - unpacking…
Andrew
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4 answers

File I/O error using nglview.show_biopython(structure)

So I have been trying to get into visualizing proteins in python, so after some research I ended up on a tutorial that was teaching you how to visualize a protein from the COVID-19 virus, so I went and setup anaconda, got jupyter notebook working in…
Jeremiah Wade
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Modification time does not trigger a snakemake rule

I'm trying to use snakemake to replace some make workflows, but I'm finding that snakemake does not use the file modification time to trigger a rule. Here is my snakefile rule sample: input: "a" output: "b" shell: …
Jules B
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3 answers

Ubiquitous regulation of highly specific marker genes

I am fairly new to scRNAseq analysis and keep running into the same problem in the two datasets I am currently working with. We work with kidney inflammation and have two new mouse models, which we are now analysing in scRNAseq. I followed the usual…
Smeerlap
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Why can't AlphaFold predict the consequences of point-mutations?

In the literature, it specifically states that AlphaFold has "Has not been trained to predict structural consequences of point mutations". See : https://alphafold.com/faq AlphaFold has not been validated for predicting the effect of mutations. In…
jambajuice
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2 answers

Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the inverse functionality as follows: from Bio.PDB import PDBParser, internal_coords #…
CubeHead
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Identify side chain atoms in BioPandas dataframe

I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python. For example, I know I could use the RMSD of all protein ATOMS in BioPandas using…
CubeHead
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Nextflow (DSL v2): how to best synchronize multiple outputs from a single process

I have a workflow that needs to: Generate .fastq files from .bams (while preserving the @RG group from the original bam) Split the .fastqs Align etc. The only way I could think to preserve the @RG group was to print it to a file during step 1 and…
Mark Ebbert
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2 answers

How do I build a glycosylated protein from PDB files manually?

I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM. How can I attach the N and O-glycans onto each protein residue with software? In PyMol, I am stuck at loading up the…
Quantumerical
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Is the algorithm of the STAR RNA Seq-Aligner similar to the Knuth-Morris-Pratt string matching algorithm?

I don't know if I'm in the right SE, if not let me know and I'll delete it. I am reading the original publication of the STAR RNA-Sequence aligner. Given the quoted text below I wonder if the algorithm for the seed search is actually an…
ilam engl
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1 answer

UPGMA computation

The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock for taxa under consideration. Two clusters $A$ and…
xxxcompbioxxx
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Why does it require 4 vectors to calculate a torsion angle?

The BioPython documentation shows the following: 11.6.3 Measuring torsion angles Use the vector representation of the atomic coordinates, and the calc dihedral function from the Vector module: >>> vector1 = atom1.get_vector() >>> vector2 =…
user366312
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Why does the SARS-Cov2 genome has letter t

ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is part of the 5'UTR of genome of an RNA virus SARS-Cov-2. RNA contains letters C+G+A+U. DNA contains letters C+G+A+T. Why are there letters T, in the SARS-Cov-2 genome, instead of U?
Pavel Pelan
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