Questions tagged [biopython]
The biopython tag has no usage guidance.
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BioPython bootstrap is not reliable?
Here i will show you a minimal working example of code and as you can see the support values for the tree is always 100.
I am using synthetic sequences of 100bp for 6 elements. The sequences have been ...
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Metabolic Modeling
I am trying to identify the flux of IgG antibody in CHO ovary cells with optimised biomass and glucose input ranging from 0 to 10, but I am not sure when I run the FBA analysis what should I define my ...
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Blastn through NCBIWWW not giving any results, as opposed to the online BLAST
I am trying to create a simple pipeline that takes a file containing various short sequences, and run them through blast. I have an example sequence;
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Getting ALL Protein entries from Entrez for a particular taxonomic id
I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command:
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retrieving past BLAST requests in bioPython
is there any way to retrieve a BLAST request made using the Biopython library using the request's query_id?
Alternatively is it possible to retrieve a query_id before the blast result is complete, and ...
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BioPython SeqIO fails with Invalid Alphabet found
I am trying to store a GenBank file that could be read by Geneious later.
I found an example how to create the GenBank file here
But now I run into Alphabet issues.
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Get SRR numbers from a GSE number
I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python.
There is an explanation for using entrez-direct on the CLI, using esearch ...
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KeyError '/n' in Bio SeqUtils Package ProtParam Script
I am trying to run a function from the ProtParam script in the Bio.SeqUtils package. The function is for calculating the instability index of a protein. The code I am using in my script with the pre-...
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Residue numbering in biopython
Is there an out-of-the-box function in the Bio.SeqIO module (in biopython) that can print a protein sequence (in command line) ...
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How to calculate the variant allelic fraction (VAF) from VEP output?
This question was also asked on Biostars
How can I calculate the variant allelic fraction from the VEP file for multiple human samples?
I used the ensembl-vep and it is human data.
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Calculation of Site Frequency Spectrum (SFS) using STR data
Hi everyone I had a question on if it is possible to calculate (Site Frequency Spectrum)SFS using STR data. Please mention if you know any programm that can be used for that!
I have tried Arlequin but ...
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How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?
This question has also been asked on Biostars
I am looking forward to getting a valuable suggestion for a bioinformatic problem.
Background:
Currently, I am performing a de novo whole genome assembly. ...
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Download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates
I am using the following code to download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates. The code seems to work when I ...
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how to do manual search on NCBI with biopython and add link to publication
I'm trying to reproduce a complex manual search on NCBI using BioPython, but obviously something is not right. My command line is not working, but I'd especially like a way to have an accurate search ...
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open and read Fasta file (raw data)
I have a big fasta.dataset file containing half a million proteins (1.0 GB). I have four lines for each protein code:
line 1:the protein code
line 2: protein ...
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How to write FASTA records using "Bio.SeqIO.write()"
Update:
Biopython document says that "Bio.SeqIO.FastaIO.FastaWriter" class is obsolete. Now my question becomes how to I use Bio.SeqIO.write() fucntion to ...
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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 ...
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Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file
As the title summarizes, I am trying to:
Read a PDB file (for example, 1enh.pdb).
Extract the backbone dihedral angles (phi, psi).
Modify the dihedral angles (phi, ...
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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 ...
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Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?
What would be the total size of all PDB files in RCSB?
Can I traverse/enumerate them one at a time using a Python script without downloading all of them to my local disk?
If YES, what would be the ...
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How to extract the protein sequences of a genbank file using R or biopython
sorry for the question, I'm trying to extract the proteins sequences from a genbank file.
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How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?
Suppose, I want to find the neighboring Hydrogen atoms of a specific C-alpha atom.
The following was my effort. However, it produces a bunch of empty lists.
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Remove Redundant Sequences from FASTA file with Biopython reducing memory footprint
I need help with my Biopython code, I am kind of new to Python and Biopython so please don't be harsh on me.
Everything started from here: Remove duplicated sequences in FASTA with Python
I answered ...
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