Questions tagged [biopython]

Biopython is a set of freely available tools for biological computation written in Python.

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1answer
32 views

Updating the GFF3 + Fasta to GeneBank code

I'm trying to convert gff3 and fasta into a gbk file for usage in Mauve. I've found a solution but the code is outdated: ...
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0answers
32 views

Teaching oneself bioinformatics

I'm interested in understanding bioinformatics and the field of de-extinction. Is it possible to self-teach oneself this field? I am starting with Gerald Karp's and A. Griffith's textbooks on cell ...
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1answer
24 views

How to extract part of protein complex separated with HEADER with two molecules from one PDB file

I have a PDB file which contain two molecules (receptor and ligand). Each molecule will have its own header. All in ONE PDB file. ‌The header of receptor section looks like this (line 1-6 of the PDB ...
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1answer
59 views

How do you replace multiple sequence names with new names using python?

I have into a dictionary some sequences. I would like to replace the sequences name for new names contained into a dataframe. ...
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0answers
13 views

Converting miRNA names to miRBase version IDs

I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example: hsa-miR-106a ---> hsa-miR-106a-5p hsa-miR-373* --> hsa-miR-373-5p hsa-miR-33 --> hsa-miR-33a-5p ...
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0answers
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Download COX1 (COI) gene via biopython using accessions for entire mitochondrial genomes

I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions. Here is one accession and here is a link to its COX1 ...
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2answers
33 views

Use biopython to align SeqRecords stored in dict

I'd like to perform multiple alignments, where a gene from each sample was read in from fasta files. The fasta file represented one sample and had multiple genes. I have read in each sample fasta file ...
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1answer
85 views

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. ...
3
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1answer
40 views

Counting hexamers in fasta sequence and identify its structure (and interruptions)

I have a lot of fasta files, each one with thousand of reads containing the hexameric motif "CCCTCT". The hexameric motif is highly continuous in most cases but interruptions may occur. I ...
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2answers
93 views

How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?

I know the algorithm for creating a Hydrogen atom and adding to a residue: ...
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1answer
59 views

How can I identify acceptor and donor atoms using BioPython?

I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy). How can I identify donor and acceptor atoms in a chain?
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1answer
32 views

How can I programmatically add Hydrogen to a PDB structure using BioPython?

I need to programmatically add Hydrogen atoms to a PDB file (say, 16PK.pdb) using BioPython. What algorithm should I use for this?
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1answer
34 views

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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1answer
12 views

How can I calculate the distance w.r.t. a beta sheet?

Suppose, I have a protein (say, 16PK). and, I want to calculate the distance between one of its alpha-carbons and the nearest beta-sheet. the distance between two strands in a beta-sheet (i, j). How ...
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0answers
16 views

Why does it require four vectors to calculate a torsion angle? [duplicate]

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: ...
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2answers
49 views

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: ...
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0answers
27 views

AttributeError: 'FeatureDB' object has no attribute 'strand'

It appers when a gene has a negative strand then I need to reverse the sequence. Unfortunately, I got the following error: ...
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1answer
41 views

creating a dictonary in Python

From the FASTA header I get the following information: ...
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1answer
41 views

How to Read SCF file in Python?

Is there any way that I can read SCF file in python like in R using sangerseqR, I have tried with Biopython, it seems it does not support this format.
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1answer
46 views

ensembldb equivalent in python

Is there a python equivalent to ensembldb? I want to get genome coordinates for a transcript (like the function transcriptToGenome) but need to do it in python. I ...
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0answers
46 views

3d model of a protein via nucleotide sequence

I really appreciate @Matteo Ferla's detailed answer to my previous question. I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
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2answers
97 views

How to make 3d model of a protein that not exist in PDB?

I'm working on nsSNPs(Non-synonymous single nucleotide polymorphisms) of protein AKAP13 whose PDB not available. I did one mutation in this protein and I want to show the effect by 3d modeling without ...
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1answer
52 views

Entrez (Biopython) esearch and efetch not returning sequence as expected

I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene. I have the following code: ...
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1answer
20 views

How to index residues by icode in biopython?

I am indexing a structure by the code below: ...
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0answers
35 views
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1answer
52 views

10bp sliding window quality score

I am having trouble creating a 10 basepair sliding window that goes through seq and trim them all 10 basepairs that have an average quality score (...
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1answer
129 views

Using Entrez.efetch() to retrive .fasta file from any NCBI database?

I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report ...
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0answers
20 views

Finding annotated counterpart after BLASTn with efetch (Biopython)

I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different genomes. I have the ...
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1answer
53 views

Biopython BioSQL error : AttributeError: 'DBSeq' object has no attribute '_data'

Hi I am playing with Biopython and BioSQL, I manage to create an MySQL database using Managing local biological databases with the BioSQL module tutorial: and load 2909 fasta sequences in it through: <...
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2answers
163 views

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 ...
4
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1answer
59 views

KeyError when getting features from a genbank file with biopython with some accessions but not others

I'm very new to python but i've been using it to extract the sequence of a gene from a genbank file. The issue is is that sometimes i'll get the output i want (prints the sequence to a file) and ...
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2answers
77 views

biopython-motifs , How can I create motif from sequences of different length?

I want to create motif of different length kmers. Following code works for kmers of same length but not different length.What to do ? ...
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0answers
39 views

BioPython - Retrieve sequence records from pubmed database

I'm assigned a task to fetch sequence records from "pubmed" database. I know this database is for publications and citations, but how can I retrieve those records from it? is that even ...
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0answers
52 views

How to extract clusters from a phylogenetic tree?

I am using Biopython Phylo and RDkit Cluster to obtain a UPGMA tree from a distance matrix of 5k x 5k entries. How can I extract clustered entry names given a number of clusters? For example, Bio....
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1answer
149 views

Biopython SeqIO check input file

Hi I am trying to learnt python3 and Biopython, I am trying to check imported fasta file before processing so far using: ...
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1answer
66 views

Creating a tab delimited column [closed]

I have a blast file produced. I executed a blast(x) command outputting both "qeseqid" and ...
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1answer
13 views

What is the best way to drop alignment artifacts in sequence objects in biopython?

I have a bunch of sequences created with Roary which I want to preprocess. When I read the sequences (genomics data) I want to translate them to protein sequences ...
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0answers
19 views

Detecting Allelic Imbalance

I am interested in detecting allelic imbalance for a credible set of SNPs. Currently, I am looking for some packages, hopefully, for Python, that can assist with this. I am aware of this R package, ...
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5answers
171 views

How to remove duplicates from a fasta file using python

I am using the following command: ...
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2answers
45 views

How to obtain desired output?

I am working on a project using the following command within nano: ...
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3answers
189 views

How to count the kmer occurrence in FASTA file considering overlapping and reverse complement?

I am using count_overlap() for counting the kmers from Biopython . Does it take the reverse complement of kmer into account? I need to count reverse complement too
1
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2answers
126 views

Extract sequences from MultiFASTA aligned file, by coordinates

I am trying to extract a specific sequence from a multifasta file, from each sequence in the aligned file. The sequences look like this, and there are 32 sequences within the multiFASTA: ...
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1answer
184 views

Why SeqIO.parse method isn't working?

I am trying to follow the tutorial from from the Biopython website here and I am right at the beginning (2.4.1), where I am trying a Simple FASTA parsing example which is ...
1
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1answer
331 views

I want to write python program to cut a DNA sequence at an EcoRI restriction site and print the two fragments after cutting

Seq = AAAAAAAAAAATTTTTTTTTTTGAATTCCCCCCCCCCCGGGGGGGGGGG Restriction site = GAATTC I want to cut the sequence at GA/ATTC I tried split method in python but It does not cut at GA/ATTC. Please help
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1answer
178 views

Nonbonded interactions on the GPU

i'm using this command gmx mdrun -deffnm nvt0 -nb gpu but got ...
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2answers
201 views

How to sort multiple FASTA files based on their content?

I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate these files into different locations based on ...
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3answers
50 views

How do I create Protein Ligand images

I was wondering how I can create images showing the bonds and the residue codes involved in the bound Protein Ligand complex obtained after Molecular Docking as depicted in the image below.
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0answers
52 views

Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
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0answers
59 views

UTR features in gbk files

I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' ...