Tag: Biopython

prody/ProDy – Giters

SYNOPSIS ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis…

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Index of /~psgendb/doc/local/biopython-1.64.old/Tests/output

Name Last modified Size Description Parent Directory   –   test_AlignIO 2014-05-29 05:23 31K   test_AlignIO_FastaIO 2014-05-29 05:23 60K   test_ClustalOmega_tool 2014-05-29 05:23 1.2K   test_Clustalw 2014-05-29 05:23 5.8K   test_Clustalw_tool 2014-05-29 05:23 1.3K   test_CodonTable 2014-05-29 05:23 21   test_CodonUsage 2014-05-29 05:23 784   test_DocSQL 2014-05-29 05:23 42  …

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Index of /~psgendb/doc/local/biopython-1.55.old/Bio/Nexus

Name Last modified Size Description Parent Directory   –   Nexus.py 2012-02-03 12:02 73K   Nexus.py.bak 2010-10-07 10:28 73K   Nexus.pyc 2011-12-13 14:38 58K   Nodes.py 2012-02-03 12:02 5.6K   Nodes.py.bak 2010-10-07 10:28 5.6K   Nodes.pyc 2011-12-13 14:38 7.4K   Trees.py 2012-02-03 12:02 36K   Trees.py.bak 2010-10-07 10:28 36K  …

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#1000359 – FTBFS: test failure: External MBEDTLS version mismatch

#1000359 – FTBFS: test failure: External MBEDTLS version mismatch – Debian Bug report logs Reported by: Stefano Rivera <stefanor@debian.org> Date: Mon, 22 Nov 2021 02:15:02 UTC Severity: serious Found in version python-biopython/1.79+dfsg-1 Fix blocked by 1000358: ncbi-blast+: Please remove the mbedtls version check Reply or subscribe to this bug. Toggle…

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Please rebuild against MBEDTLS 2.16.11

Package: ncbi-blast+ Version: 2.11.0+ds-1 Severity: normal Affects: python-biopython Running blastn outputs: Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime This causes python-biopython to FTBFS: ====================================================================== FAIL: test_blastn (test_NCBI_BLAST_tools.CheckCompleteArgList) Check all blastn arguments are supported. ———————————————————————- Traceback (most recent call last): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py”, line 420, in test_blastn self.check(“blastn”, Applications.NcbiblastnCommandline)…

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how to run CD-Search with python or biopython

how to run CD-Search with python or biopython 0 I’m now using the Biopython Entrez method to handle a great deal of sequencing. But I’m now facing a new problem,that is predicting the conserved domain in the sequence ( my sequences are DNA sequence.) I know this website: www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ….

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Index of /~psgendb/local/biopython-1.55.old/Tests/Motif

Name Last modified Size Description Parent Directory   –   Arnt.sites 2010-10-07 10:28 607   SRF.pfm 2010-10-07 10:28 144   alignace.out 2010-10-07 10:28 8.0K   mast.dna.oops.txt 2010-10-07 10:28 13K   mast.protein.oops.txt 2010-10-07 10:28 34K   mast.protein.tcm.txt 2010-10-07 10:28 16K   meme.dna.oops.txt 2010-10-07 10:28 15K   meme.out 2010-10-07 10:28 10K  …

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Index of /~psgendb/local/biopython-1.64.old/Bio/Graphics/GenomeDiagram

Name Last modified Size Description Parent Directory   –   _AbstractDrawer.py 2014-05-29 05:23 20K   _CircularDrawer.py 2014-05-29 05:23 66K   _Colors.py 2014-05-29 05:23 8.8K   _CrossLink.py 2014-05-29 05:23 3.1K   _Diagram.py 2014-05-29 05:23 19K   _Feature.py 2014-05-29 05:23 9.5K   _FeatureSet.py 2014-05-29 05:23 10K   _Graph.py 2014-05-29 05:23 8.7K  …

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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Index of /~psgendb/local/biopython-1.64.old/Bio/PDB

Name Last modified Size Description Parent Directory   –   AbstractPropertyMap.py 2014-05-29 05:23 4.0K   Atom.py 2014-05-29 05:23 10K   Chain.py 2014-05-29 05:23 3.9K   DSSP.py 2014-05-29 05:23 11K   Dice.py 2014-05-29 05:23 1.9K   Entity.py 2014-05-29 05:23 8.5K   FragmentMapper.py 2014-05-29 05:23 9.2K   HSExposure.py 2014-05-29 05:23 11K  …

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How Does One Programmatically (Python) Download Pdb Structures By Keyword

How Does One Programmatically (Python) Download Pdb Structures By Keyword 2 I would like to download all hemagglutinin structures for influenza virus from the Protein Data Bank via a python script. I have looked through the PDB and BioPython PDB package on how to do this with no luck. Does…

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How Does One Programmatically (Python) Download Pdb Structures By Keyword

How Does One Programmatically (Python) Download Pdb Structures By Keyword 2 I would like to download all hemagglutinin structures for influenza virus from the Protein Data Bank via a python script. I have looked through the PDB and BioPython PDB package on how to do this with no luck. Does…

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How does this array become this matrix?

Greetings. While studying clustering analysis, I got a question which about Distance matrix. In Biopython example code, import numpy as np import pandas as pd from Bio.Cluster import distancematrix data=np.array([[0, 1, 2, 3],[4, 5, 6, 7],[8, 9, 10, 11],[1, 2, 3, 4]]) matrix = distancematrix(data) distances = distancematrix(data, dist=”e”) print(distances)…

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python – Extract fasta files from ID list with Biopython

I am using Biopython to find sequences in a fasta file that match IDs from a .txt file comprising selected IDs. When searching for the ID names in the fasta file manually I do get hits, but the following script doesn’t find/extract any sequences: #!/usr/bin/env python3 from Bio import SeqIO…

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Two problems in Biopython Bio.PDB

I try parsing mmCIF and MMTF in PDB, but there are problem occurs. I installed Biopython 1.78. First problem is: from Bio.PDB.MMCIFParser import MMCIFParser parser = MMCIFParser() structure = parser.get_structure(“1fat”, “1fat.cif”) print(structure) # FileNotFoundError: [Errno 2] No such file or directory: ‘1fat.cif’ when I tried parse mmCIF and PDB file,…

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python – Error while parsing gene bank file using Biopython

This question was migrated from Unix & Linux Stack Exchange because it can be answered on Bioinformatics Stack Exchange. Migrated 8 hours ago. I am trying to extract the protein sequence of specific genes from gene bank like format file obtained from antismash part of which looks like…

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entrez – 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 gene, which I found manually on that page. I have downloaded…

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How to create motifs using biopython when the sequence object contain gaps (-)?

How to create motifs using biopython when the sequence object contain gaps (-)? 0 I have a gapped candidate promoter sequence for motif predictions. I am expecting to get two motifs, 1) left side motif, 2) right side motif. For the task, I am using biopython. Following is my code….

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Biopython download nucleotide records without sequences (or skip huge sequences)

I am trying to download information from NCBI Entrez databases (nucleotide), using Biopython package. I don’t need molecular data at all. I just want to check the textual information about certain records, to see references, authors, journals, and information about voucher specimens from which the genome sample was extracted. My…

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Biopython separate gap score functions for border/internal gaps

Biopython separate gap score functions for border/internal gaps 0 Hi, I would like to define different gap score functions for left/right/internal gaps in Biopython. After reading the documentation (biopython.org/DIST/docs/tutorial/Tutorial.html#sec101, section 6.6.2.5), I found out I can define a gap scoring function for a Bio.Align.PairwiseAligner object. However, it seems like only…

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Presence absence matrix from blast results

Presence absence matrix from blast results 0 I have a many blast output files of genome names, which looks like this. In the first column of the file, it contains all the identified query UIDs, I want to make a presence-absence matrix in csv format in which a column would…

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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 and now have a dictionary of genes and their samples and sequences. Here is…

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Getting premature stop codons from exonerate output?

Getting premature stop codons from exonerate output? 1 Hello, Does anyone know a good way to get premature stop codons from exonerate’s protein2genome model?? Unfortunately the Vulgar output doesn’t record stop codons. You also can’t just get the protein sequence from the genomic DNA input (in my case the target…

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Pathogen protein sequence alignment

Pathogen protein sequence alignment 0 How do I filter by taxonomy (i.e. taxid = 2 for Bacteria) using NcbiblastpCommandline in Biopython? Is there a way to do it without downloading and filtering the nr dataset manually? Are there available and downloadable protein dataset that only involves bacteria and viruses? Thanks!…

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parsing – Best way to improve my python fasta parser without using BioPython or anything else?

I am writing my own parser for fasta format. I can’t use Biopython. For now I have done this : def read_file(fasta_file): “Parse fasta file” count = 0 headers = [] sequences = [] aux = [] with open(“yeast.fna”, ‘r’) as infile: for line in infile: record = line.rstrip() if…

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do I need to install MUSCLE and ClustalW for using biopython tool?

I am studying biopython now, but some problem occurs during practice MSA. When I tried to clustalW and MUSCLE, it didn’t works. from Bio.Align.Applications import ClustalwCommandline cline = ClustalwCommandline(“clustalw2″, infile=”lactobacillus.aln”) print(cline) this is clustalW code, I just modified file path and mane. command line said this and did not occurs:…

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Biopython Seqio.Index() And Seqio.Index_Db() Very Slow For Large Sequence

Before switching to Biopython, I thought there are similar indexing features in biopython as in bioperl. However, the biopython SeqIO.index_db() and SeqIO.index() methods are so inefficient that it’s almost impossible to random access a segment of genomic sequence using biopython. I tested the performance of biopython and bioperl in retrieving…

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python – 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. gene complement(516466..532086) /gene=”rtxA” /locus_tag=”VV1_RS17390″ /old_locus_tag=”VV2_0479″ CDS complement(516466..532086) /gene=”rtxA” /locus_tag=”VV1_RS17390″ /old_locus_tag=”VV2_0479″ /inference=”COORDINATES: similar to AA sequence:RefSeq:WP_011081430.1″ /note=”Derived by automated computational analysis using gene prediction method: Protein Homology.” /codon_start=1 /transl_table=11 /product=”MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA” /protein_id=”WP_011081430.1″ /translation=”MGKPFWRSVEYFFTGNYSADDGNNSIVAIGFGGEIHAYGGDDHV…

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Relative frequencies of the nucleotides in Fasta files

Relative frequencies of the nucleotides in Fasta files 1 I have 2 fasta files (File A, File B) each one contains sequence, How can I report the relative frequencies of the nucleotides in set A and set B with python? Thanks in advance fasta • 558 views Hi check the…

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

How can I programmatically add a Hydrogen ‘Atom’ to a ‘Residue’ object? 0 I know the algorithm for creating a Hydrogen atom and adding to a residue: Point3d create_hydrogen(Point3d C, Point3d N, Point3d CA, Point3d H) { H.set(N); H -= C; H.norm(); Point3d tmp2(N); tmp2 -= CA; tmp2.norm(); H +=…

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Getting premature stop codons from exonerate output

Getting premature stop codons from exonerate output 0 Hello, I made alignments with exonerate’s protein2genome model, and I would like to count the number of stop codons in the alignment. Unfortunately the Vulgar output doesn’t record stop codons. So then I thought I might just extract the aligned protein sequence…

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Change biopython pairwise2 output format alignment ?

Change biopython pairwise2 output format alignment ? 1 You can split the resulting text output into lines, then replace the characters as needed. It is a bit hacky but provides the most flexibility. Login before adding your answer. Traffic: 1912 users visited in the last hour Read more here: Source…

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AttributeError: ‘str’ object has no attribute ‘id’ using BioPython, parsing fasta

Thanks for contributing an answer to Stack Overflow!,Connect and share knowledge within a single location that is structured and easy to search.,This script assumes a proper fasta file. It will remove all “.seq” strings at the end of any line. And in a proper fasta file, only the ID lines…

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How to automat the calculation of alignment scores (BLOSUMxx matrix based) between one short peptide sequence and 10000 other peptide sequences (using biopython)

Hi everyone and thanks in advance for any of your help. I am running into an issue recently when trying to calculate the scores of a high number of short peptide alignments (10000). I have to calculate all the alignement scores (calculation based on the BLOSUM62 matrix, but I could…

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How to download complete genome sequence in biopython entrez.esearch

I have to download only complete genome sequences from NCBI (GenBank(full) format). I am intrested in ‘complete geneome’ not ‘whole genome’.,Here is my code for Complete Genome Sequence Parsing into .FASTA files…,You will see there are only six complete E.Coli reference genomes in NCBI (www.ncbi.nlm.nih.gov/genome/167):,To help you, here are the…

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Removing gaps from fasta sequence file

Removing gaps from fasta sequence file 1 I am using python (3.6)/biopython(1.72) to read sequence files. I have an aligned sequence file in fasta format. >Human —————————-MRLRVRLLKRTWPLEVPETEPTL-RSHLRQSLLCT-IPSSTDSEHSSLQN-NEQPSL >Chimpanzee —————————-MRLRVRLLKRTWPLEVPETEPTL-RSRLRQSLLCT-IPSSTDSEHSSLQN-NEQPSL >Dog —————————-MKLRVRLQKRTWPLDLPDAEPTL-RAHLSQALLPS-LPSSTDSEHSSLQN-NDPPSL >Mouse —————————-MKLRVRLQKRTQPLEVPESEPTL-RAHLSQVLLPT-LPSSTDTEHSSLQD-NDQPSL I need to remove the gaps ‘-‘ from the file and have the result file like this:…

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genebank biopython get /chromosome=”22″ or /map=”22q13.33″

genebank biopython get /chromosome=”22″ or /map=”22q13.33″ 1 it is located in the qualifiers field of the feature from Bio import SeqIO recs = SeqIO.parse(“input.gb”, format=”genbank”) # Go over each record for rec in recs: # Go over each feature for feat in rec.features: chr = feat.qualifiers.get(“chromosome”) if chr: print (chr)…

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How to scan NCBI database using Biopython and save information as a fasta file?

How to scan NCBI database using Biopython and save information as a fasta file? 1 Hello, I am attempting to use Entrez to search the keyword “covid” in the nucleotide database and write the top 5 sequence records to a fasta file. I completed the code for question 1, but…

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Convert pdb file to table format or csv

Convert pdb file to table format or csv 0 Is there a way to convert a pdb file into a csv or table? Is there a way to parse a pdb file so that I would get atom, coordinates, atom type, residue in python dictionaries? I have been looking at…

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ncbi – How to use biopython Entrez efetch to get genbank file from “gene” database

I am trying to programmatically get whole genes ( with intron and exon structure as defined by CDS) using Biopython Entrez esearch and efetch utilities. from Bio import Entrez Entrez.email = “myemail@gmail.com” handle = Entrez.esearch(db=”gene”,retmax = “10”,term=”P53 AND Homo Sapiens [organism]”) record = Entrez.read(handle) handle_first_record = Entrez.efetch(db=”gene”,id=record[“IdList”][0],rettype=”gb”,retmode=”text”) info = handle.read()…

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Multiple Sequence Alignment using Biopython

Multiple Sequence Alignment using Biopython 0 Hello, I have one fasta file with four different sequences in it. The command I am instructed to use is pairwise2 in biopython. How can I set up a code that performs pairwise global sequence alignment between each pair of sequences in the fasta…

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Accepted python-biopython 1.79+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 22 Oct 2021 18:10:48 +0200 Source: python-biopython Architecture: source Version: 1.79+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: python-biopython (1.79+dfsg-1) unstable; urgency=medium . * Migrate from Experimental to Unstable. * Mark spelling.patch…

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How can I calculate the distance between a C-alpha atom and its hydrogen bond in a protein?

How can I calculate the distance between a C-alpha atom and its hydrogen bond in a protein? 0 I need to calculate the distance between a given C-alpha atom and the Hydrogen bonds in a protein in BioPython. And, I need to calculate that from a PDB file. Can anyone…

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Biopython’s Esearch for Pubmed does not give the same results as web search

I can think of two factors that might cause different results between Biopython and the web search: Depending on how specific the query you give Biopython is, it will be translated before retrieving results. Example: <sclerosis> will be translated to <“sclerosis”[MeSH Terms] OR “sclerosis”[All Fields]> As GenoMax pointed out, the…

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Cant make blastn work using biopython and NCBIWWW qblast, any thoughts?

Hello all, I’m a beginner level python user experiencing a problem using biopython. I’m taking an online bioinformatics course and the example that we’re working through right now is to take a fasta file (called myseq.fa in the following example), open it then read. Then using the NCBIWWW module we…

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autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

Source: ncbi-acc-download Version: 0.2.7-1 Severity: important Tags: ftbfs Dear Maintainer, I am trying to assess the side effects of an upgrade of the package python-biopython to 1.79 to its reverse dependencies. Pseudo-excuses look alright, except for ncbi-acc-download [1]. [1]: release.debian.org/britney/pseudo-excuses-experimental.html [2]: ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz The full log [2] shows variations around the…

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Extracting named fasta sequences according to list with Biopython

Extracting named fasta sequences according to list with Biopython 0 Hi all, I’m trying to work out a quick script to extract a set of sequence fasta files from a multifasta and write them all to a new, single fasta file. To elaborate, I’ve got a proteome, and I want…

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Accesing reference genome from Genome database (ncbi) with biopython

Accesing reference genome from Genome database (ncbi) with biopython 1 Hello all, I would like to acces to the reference genome RefSeq UID given a taxonomy id using the Genome database with biopython. I will try to explain with images what I mean. I search in the Genome database using…

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Accepted python-biopython 1.79+dfsg-1~0exp0 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 16 Oct 2021 12:30:51 +0200 Source: python-biopython Architecture: source Version: 1.79+dfsg-1~0exp0 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: python-biopython (1.79+dfsg-1~0exp0) experimental; urgency=medium . * New upstream version * d/copyright: update years per…

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Index of /~psgendb/local/biopython-1.55.old/Bio/AlignAce

Name Last modified Size Description Parent Directory   –   AlignAceStandalone.py 2012-02-03 12:02 2.3K   AlignAceStandalone.p..> 2010-10-07 10:28 2.3K   Applications.py 2010-10-07 10:28 2.5K   CompareAceStandalone.py 2012-02-03 12:02 1.1K   CompareAceStandalone..> 2010-10-07 10:28 1.1K   Motif.py 2012-02-03 12:02 8.7K   Motif.py.bak 2010-10-07 10:28 8.6K   Parser.py 2012-02-03 12:02 3.3K  …

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Learn Biopython: Preliminary Step Toward Bioinformatics

MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 Ch Genre: eLearning | Language: English + .srt | Duration: 32 lectures (2h 28m) | Size: 815 MB Performing the Daily Tasks of Bioinformatics What you’ll learn: The basics of Python and Biopython Requirements There are no requirements except…

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How to merge exons based on gene ids?

Since this is still unanswered, I’ll post an R solution until someone is kind enough to answer with the requested biopython solution. Read the fasta file in. library(“Biostrings”) library(“tidyverse”) fasta <- readDNAStringSet(“test.fasta”) You’ll end up with a Biostrings object of the fasta file. > fasta DNAStringSet object of length 7:…

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nlp – What is the algorithm behind pairwise2 align in BioPython?

The package BioPython allows to compute pairwise local or global alignement, through different functions (align.globalxx, align.localxx, …). However, I have not found anywhere the algorithm on which this alignement is based. The code (source, doc) states: “Pairwise sequence alignment using a dynamic programming algorithm”, and that is all. Is there…

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Blast applications analysis at MainKeys

add to compare Best Penny Stock, Best SEO Company New York, Marketing Company New York blastapplications.com Blastapplications is one of the largest Best Penny Stock New York, Best SEO Company New York, Marketing Company New York best seo company new York. And much more. 0  add to compare InvestorsHub –…

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Extract SS with chain WITHOUT Biopython

Extract SS with chain WITHOUT Biopython 0 Hello, I have a list of 150 DSSP files from 150 PDB IDs with their chain that I need to obtain the SS from that are specific to the chain in question. I need to create a simple for loop by opening the…

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python-reportlab breaks autopkgtest of python-biopython

Processing control commands: > found -1 python-reportlab/3.5.67-2 Bug #995689 [src:python-reportlab, src:python-biopython] python-reportlab breaks autopkgtest of python-biopython Marked as found in versions python-reportlab/3.5.67-2. > found -1 python-biopython/1.78+dfsg-5 Bug #995689 [src:python-reportlab, src:python-biopython] python-reportlab breaks autopkgtest of python-biopython Marked as found in versions python-biopython/1.78+dfsg-5. — 995689: bugs.debian.org/cgi-bin/bugreport.cgi?bug=995689 Debian Bug Tracking System Contact ow…@bugs.debian.org

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how to get secondary structure from DSSP?

Here is Biopython’s DSSP code, with typical use shown near the top. It is not difficult to extract this information on your own by reading contents of column 17 of the DSSP output, following this line: # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H–>O O–>H-N N-H–>O O–>H-N TCO KAPPA ALPHA…

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Help extracting SS from DSSP file

Help extracting SS from DSSP file 0 Hello, I am new to programming but need some help extracting SSS from specific chains from 150 dssp files. Any help would be appreciated. I would like to do it in python, I am aware there is a biopython parser from dssp files,…

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Capri Criteria For Evaluating Docked Protein Complexes

In our lab we use Profit (www.bioinf.org.uk/software/profit/) for the ligand and interface RMSD calculations. Depending on the complexity of your system this might be easy or not at all. The steps we take are: 1 – Define an interface region between both chains in the native structure. Basically, check for…

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Sequence similarity networks with python

Sequence similarity networks with python 1 How to build sequence similarity networks within python? Pythoscape seems no longer available and biopython pairwise does not seem the most suitable for thousands of sequences. Any ideas? Thank you sequence networks similarity • 29 views There are lots of algorithms out there for…

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GitHub – emanuil-tolev/wellcome-outputs-from-ncbi: Python script(s) which use Biopython to get a unique list of Wellcome Trust research outputs from NCBI (PubMed

GitHub – emanuil-tolev/wellcome-outputs-from-ncbi: Python script(s) which use Biopython to get a unique list of Wellcome Trust research outputs from NCBI (PubMed – using the Entrez Eutils API). Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time Python script(s) which use Biopython to get a…

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Correct Way To Parse A Fasta File In Python

Correct Way To Parse A Fasta File In Python 8 Hi, I have been wondering at the correct approach in Python, maybe using Biopython, of parsing a fasta file without having to place it in memory (eg: NOT having to read it to a list, dictionary or fasta class) before…

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package does not ship resource files

Control: found -1 38.90+dfsg-1 Control: tag -1 confirmed Hi all, Andreas Tille, on 2021-09-30: > Am Thu, Sep 30, 2021 at 01:22:23PM -0400 schrieb Robert: > > The bbmap package does not ship the needed resource files which causes some > > of > > the included tools not to…

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install biopython jupyter

like BLAST, ClustalW, FASTA, GenBank, PubMed ExPASy, SwissProt, and many more. conda install-c conda-forge ipyleaflet With pip: pip install ipyleaflet If you are using the classic Jupyter Notebook >> import Bio >>> Bio.__version__. For Windows we provide click-and-run installers. The easiest way to install statsmodels is to install it as…

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biopython write fasta

Step 1 − Create a file named blast_example.fasta in the Biopython directory and give the below sequence information as input. 3. “””Bio.SeqIO support for the “fasta” (aka FastA or Pearson) file format. Then we save this line of text to the output file: Now we have finished all the genes,…

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genbank submission tutorial

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. Finally, make sure the Include Primers box is unchecked, as we are not submitting primers with this sequence. Influenza virus sequences. September, 2008. Please download the current version. Some mitochondrial genomes contain CDS’s that…

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How to verify putative miRNA

How to verify putative miRNA 1 My PI gave me a list of some DNA sequences, each one around 25 nucleotides, that are suspected to code for Vitis Vitinesfera miRNA. To know if they are complementary to some mRNA for a known protein sequence, we do the following process: BLAST…

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Uni Roles Australia: Grant-Funded Researcher, Bioinformatics

(Level A) $89,610 to $96,007 per annum and (Level B) $100,933 to $119,391 per annum plus an employer contribution of up to 17% superannuation may apply Two fixed-term, full-time positions available for three years Two exciting Bioinformatic opportunities in the newly established Adelaide Centre for Epigenetics (ACE) These two positions…

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biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

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Biopython Biopython Statistics & Issues

Issue Title State Comments Created Date Updated Date Closed Date Add .islower() and .isupper() methods to Seq? open 0 2021-09-25 2021-09-18 – Apparently random fluctuations in coverage via CodeCov? open 1 2021-09-23 2021-09-18 – BgzfWriter accepts read-only fileobj open 1 2021-09-23 2021-09-18 – BgzfReader argument `mode` not tested if a…

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

solution from @sören: I came up with this solution for my problem: from Bio.KEGG import REST as kegg def _get_kegg(kegg_id): kegg_output = kegg.kegg_get(kegg_id).read() results = {} for line in kegg_output.split(‘n’): splits = line.split() if not line.startswith(‘ ‘): if len(splits) > 0: key = splits[0] value=” “.join(splits[1:]) results[key] = value else:…

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Failure to parse origin-spanning features

Setup I am reporting a problem with Biopython version, Python version, and operatingsystem as follows: 3.9.6 (default, Jun 29 2021, 06:20:32) [Clang 12.0.0 (clang-1200.0.32.29)] CPython macOS-10.15.7-x86_64-i386-64bit 1.79 Expected vs. Actual behaviour Loading the attached GenBank file (renamed for upload to GitHub): pME_B_0_08_0005_Akan(Vn)_(sfgfp).gb.txtdiscards the origin-spanning feature as being from an undefined…

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Python program to find the indexes of Cys in the given mutlifasta sequences

Python program to find the indexes of Cys in the given mutlifasta sequences 1 fasta = open(‘out.fa’, ‘r+’) for line in fasta.read().split(‘n’): if line.startswith(“>”): header = line print(header) else: indexes = [] for i in range(0, len(line)-1): if line[i] == ‘C’: indexes.append(i+1) print(“Cys : “, indexes) a indexes file given…

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extracting gene names

extracting gene names 1 I extracted bunch of abstracts from pubmed using the Entrez module. now I have the bunch of abstracts with me from this abstracts I want to extract gene names which are avilable in that abstracts. would anyone say he solution for this problem biopython python r…

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Dna Research Using Biopython | Free eBooks Download

Category: Tutorial Posted on 2021-09-21, by raymanhero. Description DNA Research using BiopythonMP4 | Video: AVC 1280×720 | Audio: AAC 44KHz 2ch | Duration: 1 Hours | Lec: 9 | 400 MBGenre: eLearning | Language: English =============== An Introduction To Bioinformatics DNA Research using Biopython, An Introduction To Bioinformatics, is a…

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Need help reading Newick trees with Biopython : bioinformatics

Hey all, I am stuck on a Rosalind problem which involved reading Newick trees. I am using Biopython to parse the Newick format trees, and attempting to determine the distance between two given nodes. The only issue is that all of my Newick trees are unweighted, and as a result,…

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Biopython Contact Us | Contact Information Finder

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

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Percent identity matrix from ClustalOmega/Clustalw with Biopython

I have a set of sequences for the YPR193C coding sequence from various yeast strains. I would like to get the percent identity matrix from multiple sequence alignments using ClustalW, Clustal Omega, or MUSCLE using the Biopython wrappers. This should be possible for ClustalW and Clustal Omega based on the…

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Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

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bioinformatics – Why is the output file from Biopython not found?

cline in your code is an instance of MuscleCommandline object that you initialized with all the parameters. After the initialization, this instance can run muscle, but it will only do that if you call it. That means you have to invoke cline() When you simply print the cline object, it…

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What is the correct syntax for BioPythons SeqIO.parse()

What is the correct syntax for BioPythons SeqIO.parse() 0 When reading in an assembly with BioPython’s SeqIO the tutorial indicated when reading in multiple records one should do the following: records = list(SeqIO.parse(“somefile.fasta”, “fasta”)) This produces the expected behaviour of a subscriptable list of records. However this syntax also functions…

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How to run local BLAST (Standalone NCBI BLAST+) with Python?

How to run local BLAST (Standalone NCBI BLAST+) with Python? 1 Hello, I’m new here, but I can’t find answer in other topics. I want to run blast nucelotide, align two sequences using blast (megablast, all options default) amd check their % ident. I have installed locally – Standalone NCBI…

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Remote blast query limit

Remote blast query limit 0 Hello! How many blast queries can be processed by remote blast calls with biopython’s Bio.Blast.NCBIWWW.qblast or BLAST+ with -remote flag? When I go above 1 sequence I get the following message near the top of my XML results file (and no results: internal_error: (Severe Error)…

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Incubator for useful bioinformatics code, primarily in Python and R

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and documents in this repository are freely available for all uses. Code is available under the MIT license and images, documentations and talks under the Creative Commons No…

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Extracting coordinates of possibly H bonded solvent molecule using BioPython

Extracting coordinates of possibly H bonded solvent molecule using BioPython 0 Hi, I am trying to extract the coordinates of solvent molecule from a peptide PDB, within a distance of 3 ang of O and N atoms in peptide. Using VMD, I can extract up to 3 ang of peptide….

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parsing gbk files (antismash result)

parsing gbk files (antismash result) 0 Hello I used antismash from the CLI and I got 700 gbk files (1 gbk file per each analyzed genome). I used the following script to retrieve the predicted products from the gbk files: from Bio import SeqIO import glob for files in glob.glob(“*.gbk”):…

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Public-Health-Bioinformatics/FastaUploader: A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API

A tool for batch processing large fasta files and accompanying metadata table to repositories via API The python fasta_uploader.py script breaks large fasta files (e.g. 500mb) and related (one-to-one) tab-delimited sample contextual data into smaller batches of 1000 or some specified # of records which can then be uploaded to…

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A Biopython-based method for comprehensively searching for eponyms in Pubmed

doi: 10.1016/j.mex.2021.101264. eCollection 2021. Affiliations Expand Affiliations 1 Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA. 2 Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. 3 Department of Pathology and the Eugene McDermott Center for Human…

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Sorting and writing multifasta entries to new fasta files

Sorting and writing multifasta entries to new fasta files 0 Hi, first post here. So I’m trying take the CDS out of various species’ orthologous sequences. I’m running on a Linux server, and am mainly aiming to use BioPython or Linux programs for this. I’ve run OrthoFinder on 28 species…

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Python FASTA scripting

Python FASTA scripting 4 Hi all, I finally got that illusive Bioinformatician job and am now undergoing training. My first project is to write a FASTA parsing script that will take a FASTA file and split it into multiple files each containing a gene and its sequence. The task is…

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Seqio.Parse Some Error

Seqio.Parse Some Error 2 I am a beginner in bioinformatics world. I am following exercise on biopython but i am stuck here. I am not sure why print command is not working. Please let me know to correct this step. > from Bio import SeqIO > for seq_record in SeqIO.parse(“…

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Accepted python-biopython 1.78+dfsg-5 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sun, 22 Aug 2021 21:56:28 +0200 Source: python-biopython Architecture: source Version: 1.78+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 986410 Changes: python-biopython (1.78+dfsg-5) unstable; urgency=medium . * d/control: update uploader address * d/watch:…

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More than one archive specified. Try –help.

Package: routine-update Version: 0.0.6 Severity: important Hi Andreas, when working on making sure the python-biopython watch file was appropriately fixed, I saw routine-update choke with the following error: $ routine-update gbp:info: Fetching from default remote for each branch gbp:info: Branch ‘master’ is already up to date. gbp:info: Branch ‘pristine-tar’ is already up to date. gbp:info: Branch…

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Get gene sequence for oragnism using python

Get gene sequence for oragnism using python 0 Hi , If i have the Genus & Species how can i use them in python code to get a gene sequence. For example: SpecCode: 64588 Genus: Aapticheilichthys Species: websteri How can i use these date to get “Cox1” sequence in python…

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Search PDB-format files for residue contacts

Search PDB-format files for residue contacts 1 I am looking for a program that can process a large number of protein stuctures (PDB-format) and search the coordinates for a given criterion, or better, a combination of such criteria. A possible query would be: “return all instances where a lysine epsilon…

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Is there a way to separate the chains belong to each Biological assembly in a PDB file?

Is there a way to separate the chains belong to each Biological assembly in a PDB file? 1 I want to separate the chain IDs which belong to specific Biological assemblies in a PDB file. As an Example PDB ID 1BRS has 3 Biological assemblies Biological assembly 1 : –…

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biopython | DelphiFeeds.com

biopython | DelphiFeeds.com Story Category: biopython Hands-On Bioinformatics With These 6 Powerful Python Libs Muhammad Azizul Hakim Are you looking for tools to work in Bioinformatics…

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Fastest way to perform BLAST search using a multi-FASTA file against a remote database

Fastest way to perform BLAST search using a multi-FASTA file against a remote database 0 I have a multi-FASTA file having ~125 protein sequences. I need to perform a BLASTP seach against remote nr database. I tried using NcbiblastpCommandline, but the issue is that it only accepts files as input….

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Find most similar peptide and calculate distance?

Find most similar peptide and calculate distance? 0 Hello! I have mutant and wild peptide. I select some short subpeptide containing mutation and i want to find the most similar subpeptide (preferably of the same length) in the wild peptide to compare its immunological properties to the mutant one. And…

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Issue reading fasta file with Biopython

Hello everyone, This should be very easy and I know it, but I am stuck with it and I cannot pinpoint my mistake. I wanted a boolean python function to check if a given file is in fasta format. And this, without manually checking myself the extension (.fa, .fasta etc)….

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