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Questions tagged [biopython]

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

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2answers
59 views

read and matching pattern with python

I have read the content of a text file into pandas and needed some help matching the pattern. Here is the pattern, where a can any number greater than zero and <...
2
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0answers
19 views

How to load output from the kegg API in biopython into a pandas dataframe?

Biopython provides a (bit unintuitive) API to access KEGG. I am trying to make use of it, but the output is quite unhandy as a string. What is the best way to parse the data into a ...
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1answer
31 views

Biopython Genbank writer not splitting long lines

I am parsing a csv file of annotated sequences and using Biopython to generate Genbank files for each. I want to add annotations of the sequence features. My output file shows features listed without ...
2
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1answer
36 views

Parsing specific features from Genbank by label?

I'm trying to parse a Genbank file to find a specific feature. I can pull it out if I know the feature type (e.g. repeat_region). E.g. if I'm looking for this feature: ...
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1answer
43 views

From ensembl id to protein structure

Forgive me if this question is too trivial. I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this? Is there any script(python, R) so that ...
1
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1answer
45 views

I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets (human). I only have their protein symbols. As an example: EGFR AR FOXA1 CXCR3 ... I want to get structural data (atomic coordinate) from PDB (Protein ...
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2answers
76 views

Biopython Failure to break out of loop

After qblast, I wanted to print only details from the first 3 BLAST output. Yet, the code below printed the details of every BLAST output. Why can't I break out of the loop to achieve my desired ...
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2answers
77 views

How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
3
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1answer
31 views

How to select only RNA with Hetero atoms from pdb file with python?

I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
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0answers
37 views

How to compare multiple genetic profiles in Python?

I have hundreds of vcf file where each vcf file contains genome profile for a tissue. A portion of the vcf file is as follows: [ I can read each vcf file into a dataframe. So it would be hundreds of ...
4
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1answer
125 views

HDF5 and BioSQL solutions

I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data ...
1
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1answer
139 views

What do negative dN or dS mean in cal_dn_ds in Biopython?

I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
3
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1answer
89 views

How to learn/get started bioinformatics? [closed]

I know this is a broad question and I'm sorry if this is not the right place to post (this is my first post ever), but is there some sort of roadmap for bioinformatics? I'm an undergraduate student ...
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1answer
38 views

Retrieve ID ligand from PDB file

I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex. Is there a way to do that ...
1
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1answer
55 views

How to get Uniprot and swissprot cross references using Biopython

I am struggling to use biopython to gather cross references such as GO annotation from Uniprot/swissprot text files ("DR" in the .txt files) using biopython. From ...
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1answer
41 views

How to allow “half windows” in biopython?

I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
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0answers
66 views

How to get bootstrap support of phylogenetic tree?

I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" ...
7
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2answers
122 views

Truncating branch length values of Phylogenetic tree with biopython

I have been using biopython 1.72 to display my phylogenetic tree files. 1)Using the function 'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to ...
5
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1answer
103 views

How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file

Context I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites: <...
7
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3answers
126 views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
2
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0answers
474 views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
2
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1answer
88 views

Counting the characters in a row using python

I am using python 3 and biopython 1.72. I have been using a protein sequence file in clustal format. ...
6
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1answer
89 views

Getting all NNI trees of a parsimony tree

I have an aligned protein sequence file which I have been using for reconstructing a parsimonious tree. I am currently using NNITreeSearcher._get_neighbors method from Biopython 1.72 but it's way to ...
5
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2answers
100 views

Counting letters in phylip alignment columns with Biopython

I have been using python 3.6 and biopython 1.72 to work with protein data files. I am using a protein sequence file (phylip format), for example: ...
2
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2answers
91 views

Get a list of PDB ids from a list of sequence protein number?

I am working on a project about phosphorylation, and I am creating a database of some proteins. I have a list of protein accession ids for which I need to get the corresponding PDB file for each one ...
4
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1answer
176 views

Get results of keyword search on Pfam via python script

I'm interested in all proteins that are in any way associated with Danio rerio. I decided to look them up at Pfam data base and when I just make a keyword search, I get a a nice list which looks like ...
3
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0answers
84 views

Glocal\semi-local\Hybride Globale-Local alignment with Python

I was looking for a simple way to do a glocal alignment. The case I have is I have a small sequence which should be find in a bigger one, thus typically a glocal alignment. Also I can not Install ...
0
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1answer
91 views

Find a map/correspondence between two versions of a genome

I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in ...
3
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1answer
118 views

How to assess the quality of assembled .fasta genome files?

I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens. I would like to see if the assembled ...
2
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2answers
200 views

Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession

I have about 10,000 genome files all named by either refseq or genbank accession number, do you know if it's possible to convert these numbers to the corresponding NCBI taxon ID or species? for ...
2
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1answer
87 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
3
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1answer
347 views

How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as ...
14
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1answer
561 views

Biopython Phylogenetic Tree replace branch tip labels by sequence logos

Having recently constructed a lot of phylogenetic trees with the module TreeConstruction from Phylo package from Biopython, I've been asked to replace the branch tip labels by the corresponding ...
4
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1answer
171 views

Finding proteins in a sequence

I have a file with protein sequences, all on a single line, like this: ...
1
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2answers
82 views

obtaining identifier from plot of sequence GC%

I was looking at this script from http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297 and wanted to use it to determine outliers for tentative Horizontal gene transfer. The data set is ...
4
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1answer
138 views

How can I reproduce a manual NCBI search with Biopython Entrez module?

I'm trying to make a Biopython script that reproduces a manual search on the NCBI website. My manual search gives me the following URL: https://www.ncbi.nlm.nih.gov/nuccore?term=ANOS1[gene%20name]%...
4
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0answers
159 views

How to find which scales are available in SeqUtil of Biopython?

I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil". ...
7
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2answers
427 views

Is there a standard way to clean a PDB file and re-number its residues?

Is there a pre-existing tool which will tidy up the numbering of a PDB file? Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
2
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1answer
316 views

getting KeyError on certain residues in BioPython: ATOM vs. HETATM lines

When I want to load atoms for residuum (' ', 85, ' ') in chain A for protein 3tmm with structure[0][chain_id][residue], but I'm ...
5
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1answer
202 views

Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?

On this Biopython tutorial, they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module: ...
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0answers
269 views

Biopython - extracting query coverage from XML Blast output

I need to extract (or to calculate precisely) the query coverage from Blast output. Now I use NCBIWWW.qblast to query Blast in XML format. Is it possible to know the query coverage parsing the XML ...
4
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2answers
365 views

Finding a single open reading frame with ribosomal binding site, using Biopython

I'm given a Fasta file, containing a large DNA(over 115,000 long) sequence, and I am tasked with finding a single large open reading frame contained within the DNA sequence using Biopython. I'm ...
0
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0answers
86 views

Finding a single open reading frame with ribosomal binding site, using Biopython [duplicate]

I'm given a Fasta file, containing a large DNA(over 115,000 long) sequence, and I am tasked with finding a single large open reading frame contained within the DNA sequence using Biopython. I'm ...
3
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1answer
265 views

How can I apply proportional (p) distances (Nucleotide) using bioPython

I am working on phylogenetic tree generation. I used BioPython and ClustalW 2.x.x for this purpose. I have generate the tree using BioPython but when I try to generate tree using "MegaSoftware GUI" ...
3
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1answer
43 views

Automating sequence download from Wormbase

I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase. I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
9
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5answers
2k views

How do I find identical sequences in a FASTA file?

I want to create a database for a proteomics study. Therefore, the mapping from a given sequence to a protein ID has to be unique. I am wondering whether there is already a built-in function in ...
1
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1answer
217 views

Filtering out all seqs with mutations of list2 from list1

I have 2 lists, list1 and list2, of protein sequences of the same given gene in different strains. In ...
0
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1answer
70 views

Biopython code refactoring

I want to make function get_abstract, but i don't know what this can look like if the function must return idlist. ...
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2answers
272 views

Mutations in sequences relative to reference (histogram)

I have a reference sequence of amino acids that I compare other sequences to using Bio.pairwise2.align.globalmx of Biopython package (one to many compare - one by ...
4
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2answers
756 views

How to map PDB chains to Uniprot IDs using API services

I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...