Tag: Biopython

Get mRNA sequence from amino acid sequence using BioPython

Get mRNA sequence from amino acid sequence using BioPython 1 I have a sequence of amino acids like “MVLLV” and I want to know what mRNA corresponds to that, I’m using biopython for this, but I just know the back_transcribe(), to revert the RNA to DNA, how can I do…

Continue Reading Get mRNA sequence from amino acid sequence using BioPython

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

Continue Reading A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

How to Analyze Coronavirus RNA with Python (Part 2: Installing Biopython) | by Proto Bioengineering | Feb, 2024

The Biopython logo Biopython is a set of tools for doing all sorts of genomics tasks: reading DNA and RNA, aligning sequences, analyzing similarities between sequences, and more. This is the second part in a series on analyzing coronavirus RNA with Python. Here we’ll install Biopython and use it to…

Continue Reading How to Analyze Coronavirus RNA with Python (Part 2: Installing Biopython) | by Proto Bioengineering | Feb, 2024

From nucleotide or proteine sequences to EC number using biopython

From nucleotide or proteine sequences to EC number using biopython 0 Hi, if I have a fasta file containing nucleotide sequences or proteines sequences is it possible to get EC number using biopython for example 1.1.1.169 1.1.1.205 1.1.1.25 1.1.1.302 1.1.1.330 1.1.1.34 ps : I’m working on fungus so I need…

Continue Reading From nucleotide or proteine sequences to EC number using biopython

Accepted python-biopython 1.81+dfsg-3 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 19 Dec 2023 15:06:46 +0100 Source: python-biopython Architecture: source Version: 1.81+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1058967 Changes: python-biopython (1.81+dfsg-3) unstable; urgency=medium . * d/control: remove dependency on python3-unittest2. (Closes:…

Continue Reading Accepted python-biopython 1.81+dfsg-3 (source) into unstable

Python Biopython Biological Sequences – CodePal

This function utilizes Biopython, a powerful and widely-used Python library for working with biological sequences, to read, write, and manipulate biological sequences. The function takes a file path to an input file containing a biological sequence, reads the sequence using Biopython’s SeqIO module, manipulates the sequence, and writes the manipulated…

Continue Reading Python Biopython Biological Sequences – CodePal

How to query NCBI to extract Virus fasta files using BioPython?

How to query NCBI to extract Virus fasta files using BioPython? 1 Hi ! I want to extract the genome fasta files of 30 samples automatically using python script from here www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&host=bacteria. I want the virusus that have has host bacteria and I am using BioPython Package. Entrez.email = “mail”…

Continue Reading How to query NCBI to extract Virus fasta files using BioPython?

Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files

Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files 0 Hi, Does anyone know if there’s an existing tool to calculate genetic distances between query and subject sequences in BAMs/SAMs? I’m reasonably sure it’s possible to identify transitions and transversions using data from the MD flag and the sequence, and…

Continue Reading Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files

How can I obtain the DNA sequences of each CDS for several genbank files?

How can I obtain the DNA sequences of each CDS for several genbank files? 0 Hello, I want to obtain DNA sequences of all the CDS from multiple genbank files in one fasta file. I tried several solutions with Biopython but nothing is working for me. I tried for exemple…

Continue Reading How can I obtain the DNA sequences of each CDS for several genbank files?

sequence alignment – BioPython bootstrap is not reliable?

I think this is a bug. It seems to work if you do this, creating an equivalent Alignment object instead of a MultipleSeqAlignment to give the bootstrap step: from Bio.Align import Alignment alignment2 = Alignment(list(alignment)) consensus_tree = bootstrap_consensus(alignment=alignment2, times=50, tree_constructor=constructor, consensus=majority_consensus) bootstrap_consensus calls bootstrap_trees, which makes however many randomly shuffled…

Continue Reading sequence alignment – BioPython bootstrap is not reliable?

Calculate GC content for entire chromosome

If you’re comfortable using Python, I’ve created a script that calculates the GC content and GC-skew for each contig, scaffold, or chromosome in a fasta file. This is specifically designed for generating data for a circos plot. To use the script, make sure you have Biopython installed in your conda…

Continue Reading Calculate GC content for entire chromosome

BioPython | Oxford Protein Informatics Group

Pandas is one of the most used packages for data analysis in python. The library provides functionalities that allow to perfrom complex data manipulation operations in a few lines of code. However, as the number of functions provided is huge, it is impossible to keep track of all of them….

Continue Reading BioPython | Oxford Protein Informatics Group

BioSQL Unable to remove database using server.remove_database

BioSQL Unable to remove database using server.remove_database 0 Just installed the biosql and with mysql and tried to create test database with name “orchids”. It created and add some data to subdatabse via Entrez. But problem is when trying to delete whole subdatabase with using server.remove_database(“orchids”) it gives error. All…

Continue Reading BioSQL Unable to remove database using server.remove_database

python – Biopython bioSQL Unable to remove database using server.remove_database(‘dbname’)

bioSQL Unable to remove database using server.remove_database(‘dbname’) Just installed the biosql and with mysql and tried to create test database with name “orchids”. It created and add some data to subdatabse via Entrez. But problem is when trying to delete whole subdatabase with using server.remove_database(“orchids”) it gives error. All codes…

Continue Reading python – Biopython bioSQL Unable to remove database using server.remove_database(‘dbname’)

Python function to export the annotated records to genbank file using python and biopython

Python function to export the annotated records to genbank file using python and biopython 0 def export_annotated_data(annotated_records, output_file): Convert records to genbank format SeqIO.write(annotated_records, output_file, “genbank”) it throws an error of str ‘name’ missing biopython python bioinformatic programming • 20 views • link updated 1 minute ago by barslmn &starf;…

Continue Reading Python function to export the annotated records to genbank file using python and biopython

Bioinformatics Trainer Part Time Job Opening at Biotecnika

Bioinformatics Trainer Part Time Job Opening at Biotecnika Bangalore Biotecnika Info Labs Pvt Ltd is a leading Bio-IT Company with a diversified portfolio in Information technology and biotechnology. We seek a highly motivated and experienced individual to join our team as a Part-Time Bioinformatics Trainer & Researcher. The successful candidate…

Continue Reading Bioinformatics Trainer Part Time Job Opening at Biotecnika

Integrating BLAST Searches into Data Science Projects with Biopython | by Bao Tram Duong | Nov, 2023

BLAST, or Basic Local Alignment Search Tool, is a powerful and widely used bioinformatics tool for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotide sequences of DNA. The main purpose of BLAST is to identify sequences in a database that are similar…

Continue Reading Integrating BLAST Searches into Data Science Projects with Biopython | by Bao Tram Duong | Nov, 2023

Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

Continue Reading Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Biopython is an open-source collection of Python tools for computational biology and bioinformatics. It provides modules and classes to work with biological data such as DNA, RNA, protein sequences, structures, and more. Biopython aims to make it easy for developers to access and manipulate biological data in a programmatic way….

Continue Reading Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Predicting circRNA-disease association using heterogeneous network and meta-path

[1] H. L. Sanger, G. Klotz, D. Riesner, H. J. Gross, A. K. Kleinschmidt, Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures, Proc. Natl. Acad. Sci. USA, 73 (1976), 3852–3856. doi.org/10.1073/pnas.73.11.3852 doi: 10.1073/pnas.73.11.3852 …

Continue Reading Predicting circRNA-disease association using heterogeneous network and meta-path

Accepted python-biopython 1.81+dfsg-2 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 11 Nov 2023 11:16:46 +0100 Source: python-biopython Architecture: source Version: 1.81+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1055708 Changes: python-biopython (1.81+dfsg-2) unstable; urgency=medium . * python3.12.patch: new: fix ftbfs with python3.12….

Continue Reading Accepted python-biopython 1.81+dfsg-2 (source) into unstable

Solved In this problem, we will use Biopython to translate

In this problem, we will use Biopython to translate the CDS (CoDing Squence) sequence(s) in GenBank file. First, use the retrieve_GenBank_info(id) (from the lecture notw, also given below) to save the GenBank record of Helicobacter pylori 26695. id is the id of helicobactor you found in Problem 3. Make sure…

Continue Reading Solved In this problem, we will use Biopython to translate

How to check if my sequence is DNA or Protein in BioPython?

How to check if my sequence is DNA or Protein in BioPython? 0 I’m trying to develop a script that checks whether or not the input fasta is the correct molecule type but I want it to account for ambiguous characters. Here’s what I have for reading in fasta: from…

Continue Reading How to check if my sequence is DNA or Protein in BioPython?

KWIK Scholarship For Biotech & Life Science UG & PG Students

KWIK Scholarship For Biotech & Life Science UG & PG Students Dear Future Researcher, I have some critical questions for you!  Q1. Are you getting suitable jobs after your graduation or postgraduation? Q2. Do You Think you Have enough skills and hands-on training that most Biopharma companies demand? Q3. Do…

Continue Reading KWIK Scholarship For Biotech & Life Science UG & PG Students

biopython – Python bioinformatic – Stack Overflow

Closed. This question needs debugging details. It is not currently accepting answers. Iam new to python and I am trying to do my homework . A DNA sequence consisting of 1000 nucleic acids will be created, the genes and their locations, including the start and stop codons of the gene,…

Continue Reading biopython – Python bioinformatic – Stack Overflow

Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

Continue Reading Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Biopython: Empowering Biologists with Computational Tools | by Everton Gomede, PhD | Nov, 2023

Introduction In the realm of modern biology, data analysis and computational techniques have become indispensable for researchers to extract valuable insights from the vast amount of biological data generated today. Biopython is a powerful and versatile open-source software library designed to meet the computational needs of biologists and bioinformaticians. This…

Continue Reading Biopython: Empowering Biologists with Computational Tools | by Everton Gomede, PhD | Nov, 2023

python – retrieving past BLAST requests in bioPython

python – retrieving past BLAST requests in bioPython – Bioinformatics Stack Exchange …

Continue Reading python – retrieving past BLAST requests in bioPython

biopython – 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; >some_random_sequence AAGGTTCGGTCCAAATTGAA which returns a hit for FUT3 (using the RefSeq_Gene DB and using grch38 as an entrez_query). However, when I try to run…

Continue Reading biopython – Blastn through NCBIWWW not giving any results, as opposed to the online BLAST

How to count fasta sequences efficiently using (or not ) biopython

How to count fasta sequences efficiently using (or not ) biopython 6 This is not a very memory friendly way of counting sequences from a multi fasta, any ideas to improve this? generator = SeqIO.parse(“test_fasta.fasta”,”fasta”) sizes = [len(rec) for rec in SeqIO.parse(“test_fasta.fasta”, “fasta”)] I’m avoiding using tools like grep since…

Continue Reading How to count fasta sequences efficiently using (or not ) biopython

Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species

Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol. 2021;166:2633–48. Article  CAS  PubMed  Google Scholar  Koonin EV, Dolja VV,…

Continue Reading Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species

How to install or uninstall “python3-biopython-sql” on Kali Linux ?

1. Install python3-biopython-sql package Please follow the steps below to install python3-biopython-sql package: sudo apt install python3-biopython-sql Copy 2. Uninstall / Remove python3-biopython-sql package Please follow the steps below to uninstall python3-biopython-sql package: sudo apt remove python3-biopython-sql Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of python3-biopython-sql…

Continue Reading How to install or uninstall “python3-biopython-sql” on Kali Linux ?

python – 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. I tried all protein classes from the documentation, but all fail with the same error: TypeError: Invalid…

Continue Reading python – BioPython SeqIO fails with Invalid Alphabet found

Elucidata hiring Senior Bioinformatics Scientist in Bangalore, IN

About Elucidata Delivering ML-ready biomedical molecular data. Job Description Elucidata’s mission is to power drug discovery by harnessing the power of structured and unstructured biomedical data. Our state-of-the-art technology transforms data so that it is analysis-ready. Biomedical data is vast but unstandardized, hence it remains underutilized. Or as we say…

Continue Reading Elucidata hiring Senior Bioinformatics Scientist in Bangalore, IN

How to install python-biopython On Ubuntu 16.04 Lts? Uninstall and remove python-biopython Package

Quick installation of python-biopython: Step 1: Update system: sudo apt-get update Step 2: Install: python-biopython Ater updaing the OS run following command to install the packae: sudo apt-get install python-biopython Package Details Package: python-biopython Version: 1.66+dfsg-1build1 Maintainer: Ubuntu Developers Home page: biopython.org Description: Python library for bioinformatics (implemented in Python…

Continue Reading How to install python-biopython On Ubuntu 16.04 Lts? Uninstall and remove python-biopython Package

Index of /~psgendb/birchhomedir/python/biopython-1.68/Tests/Exonerate

Name Last modified Size Description Parent Directory   –   exn_22_m_affine_loca..> 2016-08-25 06:38 9.9K   exn_22_m_cdna2genome..> 2016-08-25 06:38 14K   exn_22_m_coding2codi..> 2016-08-25 06:38 18K   exn_22_m_coding2codi..> 2016-08-25 06:38 2.8K   exn_22_m_coding2geno..> 2016-08-25 06:38 18K   exn_22_m_dna2protein..> 2016-08-25 06:38 776   exn_22_m_est2genome.exn 2016-08-25 06:38 9.6K   exn_22_m_genome2geno..> 2016-08-25 06:38 10K  …

Continue Reading Index of /~psgendb/birchhomedir/python/biopython-1.68/Tests/Exonerate

How difficult is it to set up local BLAST?

How difficult is it to set up local BLAST? 1 Hello! I hope that you are doing well. I have an application that needs to perform BLAST searches. I initially was intimidated by setting up BLAST+ on my local machine. So, instead I tried to use BioPython and BLAST+ to…

Continue Reading How difficult is it to set up local BLAST?

Remote BLAST search

Remote BLAST search 2 Hello all! I hope you are doing well. I have a program that needs to make BLAST requests. However, all of the methods that I have tried are dreadfully slow. I have tried using BioPythons NCBIWWW as well as remote BLAST+, but both are horrendously slow….

Continue Reading Remote BLAST search

python – BioPython: KEGG REST keeps reporting HTTP Error 403: Forbidden – Stack Overflow

I’m attempting to use BioPython’s REST module from Bio.KEGG to query the KEGG database to get the names and formulas of some compounds, using the compounds chemical identification number (CID), e.g. C0001 is water, C00123 is leucine, etc: from Bio.KEGG import REST from Bio.KEGG import Compound def cpd_decoder(cid): #gets the…

Continue Reading python – BioPython: KEGG REST keeps reporting HTTP Error 403: Forbidden – Stack Overflow

incompatible with python3-biopython > 1.79

Source: prody Version: 2.3.1+dfsg-3 Severity: serious Justification: FTBFS Tags: sid ftbfs Forwarded: github.com/prody/ProDy/issues/1723 Hello, prody FTBFS with python3-biopython > 1.79: ====================================================================== FAIL: testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ———————————————————————- Traceback (most recent call last): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_analysis.py”, line 1210, in testBuildMSAlocal assert_array_equal(expect, result) File “/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py”, line 985, in assert_array_equal assert_array_compare(operator.__eq__, x, y, err_msg=err_msg, File “/usr/lib/python3.11/contextlib.py”,…

Continue Reading incompatible with python3-biopython > 1.79

BioPython BLAST unusable?

BioPython BLAST unusable? 0 I have been using BioPython to perform BLAST queries through NCBI. However, the speed is so slow, it is essentially unusable. The request below takes ~ 7 minutes to complete, while it only takes 11s to BLAST the same sequence using the webtool. I used the…

Continue Reading BioPython BLAST unusable?

What is the new Entrez login for NCBI API?

What is the new Entrez login for NCBI API? 0 NCBI recently offloaded logging in to other websites. How do we reliably set the email and API key variables to use Entrez with the API key? I have attempted my legacy NCBI login and it appears to timeout after too…

Continue Reading What is the new Entrez login for NCBI API?

multiple protein sequence similarity tool

multiple protein sequence similarity tool 1 Any software to find the protein sequence similarity and heatmap construction based on blast. protein-sequence • 161 views Have you tried Clustal Omega? Or you can try to search multiple sequence alignment tools, for example, in BioPython. Login before adding your answer. Read more…

Continue Reading multiple protein sequence similarity tool

Convert amino acid sequences into nucleotide sequences

How to convert amino acid sequences (big fasta files) into nucleotide sequences, any software tool? I’m using a mac. In the fasta files I have the frames too. Here’s a little example: >abc_frame=-1 SEETQLVPLGWPR*W*PWCLSPSRKTSLDLWHSNTQQCLQAAHSVHLESQFCWKCLSRY* TCSLMNLCRMYIQ*ISFQSTPVLFLQAV*SNLCSSHQENKRPDR*WSDVDLAAQSQRSAV STVHPSHMIQLPTAAELQETWFVLNLTCCE >def_frame=-2 QRKHSWSLWGGRGDGDHGAFPPVVKTPIDSQYWHSNTQQCLQAAHSVHLESQFCWKCLSR Y*TCSLMNLCSMKLQ*ISFQSTPVLFLQAV*SKL*SSHQENKRPDR*WSDVDLAAQSQRS AVSTDHPSHMIQLPTAAELQETWFVLNLTCC >ghi_frame=3 SQHVRFSTNHVSCSSAAVGSWIXCEG*TVDTADLCDCAARSTSDHHLSGLLFSW*LLXXX DQTACRKRTGVDWNEIYWSFILQRFIKEQVQYRLRHFQQNCDSKWTECAA*RHCCVLLCQ PTGRGIXGFRLLGKRHTGNSVISHPKGTNCVSS Additional info: I have a fasta…

Continue Reading Convert amino acid sequences into nucleotide sequences

Help writing code for a question on my homework

Help writing code for a question on my homework 1 Hello! I am taking my first programming class and I am struggling with some questions on my biopython homework. I can’t figure out how to work with the files and how to get the sequence from the file in order…

Continue Reading Help writing code for a question on my homework

Esearch, Epost, and Efetch for Large Datasets in Biopython

Hi, I’m working on a project that involves downloading over a million SARS-COV-2 sequences from NCBI. As this will eventually be an open source project, I’m trying to code as many steps as I can for repeatability. Currently, I’m stuck trying to use Biopython’s Entrez tools, Esearch, Epost, and Efetch…

Continue Reading Esearch, Epost, and Efetch for Large Datasets in Biopython

Scanning for ultra-hot topics in science via pubmed, or using other tools

Scanning for ultra-hot topics in science via pubmed, or using other tools 0 A search in pubmed for chatGpt returns: 0 articles in 2021 4 articles in 2022 1238 articles (as of Sept 17) in 2023 pubmed.ncbi.nlm.nih.gov/?term=chatGpt&filter=datesearch.y_10&size=100 I am not aware of a more rapid growth in scholarship relating to…

Continue Reading Scanning for ultra-hot topics in science via pubmed, or using other tools

MeiraGTx hiring Bioinformatics Analyst in New York, New York, United States

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

Continue Reading MeiraGTx hiring Bioinformatics Analyst in New York, New York, United States

How do I install DSSP?

I want to use the DSSP module in Biopython to obtain secondary structure information from a PDB file. However, even the example provided on the Biopython page(biopython.org/docs/dev/api/Bio.PDB.DSSP.html) doesn’t run. I don’t understand why I’m getting a FileNotFoundError. Because the “1ycr.pdb” file is in the same directory as my Python script….

Continue Reading How do I install DSSP?

Seeking a real project

Seeking a real project 0 I’m a Masters student in Microbial Biotech and interested in Bioinformatics. I have a handful of good skills in Bioinformatics like python programming (in a much broader sense than just using predefined scripts), biopython, pandas, R, etc. I am really good at learning such skills….

Continue Reading Seeking a real project

Not possible to install Biopython in Thonny

i get a Error message when installing Biopython in Thonny. Can someone help me please? 🙂 -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c Bio/Align/_aligners.c -o build/temp.macosx-10.9-universal2-cpython-310/Bio/Align/_aligners.o Bio/Align/_aligners.c:11:10: fatal error: ‘Python.h’ file not found #include “Python.h” ^~~~~~~~~~ 1 error generated. error: command ‘/usr/bin/clang’ failed with exit code 1 [end of output] note: This error originates from…

Continue Reading Not possible to install Biopython in Thonny

Pairwise Sequence Alignments with Numbered Antibody Sequences

Pairwise Sequence Alignments with Numbered Antibody Sequences 0 Hi All, I have been using Biopython to explore the diversity in some of my antibody sequences using a pairwise alignment. However because there are established places in the amino acid sequences where insertions and deletions may occur, there are certain numbering…

Continue Reading Pairwise Sequence Alignments with Numbered Antibody Sequences

Regulation of gene editing using T-DNA concatenation

Gelvin, S. B. Integration of Agrobacterium T-DNA into the plant genome. Annu. Rev. Genet. 51, 195–217 (2017). Article  CAS  PubMed  Google Scholar  Gelvin, S. B. Plant DNA repair and Agrobacterium T-DNA integration. Int. J. Mol. Sci. doi.org/10.3390/ijms22168458 (2021). Jupe, F. et al. The complex architecture and epigenomic impact of plant…

Continue Reading Regulation of gene editing using T-DNA concatenation

Biopython and Fab detection

Biopython and Fab detection 0 Hi there, Is there any way to detect just the Fab region of an antibody using a protein fasta file and Biopython? I was originally considering just using regex for finding conserved regions of the hinge and cutting there but was wondering if there was…

Continue Reading Biopython and Fab detection

python – Biopython initial installation tests fail

I am trying to ensure biopython has installed successfully on my windows machine. In windows powershell I call ‘pip install biopython’. Afterward I get a successfully installed message. The installation guide recommends running tests to ensure proper installation. I try running these in the “source code directory” (shown below) per…

Continue Reading python – Biopython initial installation tests fail

SRA and Bioproject IDs

SRA and Bioproject IDs 1 Dears, I have a group of Bioproject IDs and need to retrieve their corresponding SRA IDs. I tried to retrieve the whole data from SRA using kywrds <- entrez_search(db = “sra”, retmax = 20000, term = “Homo sapiens[ORGN] AND Homo sapiens[orgn:__txid9606]”) However, the result of…

Continue Reading SRA and Bioproject IDs

Library generation based on known diversity of specific residues.

Library generation based on known diversity of specific residues. 1 Hello, I am trying to figure out a way to generate a library of sequences based on known diversity at specific residues. For instance, if position 1 has 50% A and 50% C the library would have a diversity in…

Continue Reading Library generation based on known diversity of specific residues.

python – Extracting viral host from Genbank record or Entrez query

When I look up this id record on NCBI … Let’s review that record: $ curl -i ‘https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=CY238774.1&rettype=gb&retmode=text&tool=biopython’ … content-type: text/plain … FEATURES Location/Qualifiers source 1..1002 /organism=”Influenza A virus (A/Washington/27/2017(H3N2))” /mol_type=”viral cRNA” /strain=”A/Washington/27/2017″ /serotype=”H3N2″ /host=”Homo sapiens” … So we’re looking for Features –> Source –> Host. Now let’s switch to…

Continue Reading python – Extracting viral host from Genbank record or Entrez query

Bio.Phylo cut the tree (python)

Bio.Phylo cut the tree (python) 0 I have a tree and I want to cut it on a given depth (red line on the pic) to produce separate subtrees. Basically what I need is smth like the dict with group ids (1-6 on the pic) as keys and the lists…

Continue Reading Bio.Phylo cut the tree (python)

PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes

Salipante, S. J. & Horwitz, M. S. Phylogenetic fate mapping. Proc. Natl Acad. Sci. USA 103, 5448–5453 (2006). Article  CAS  PubMed  PubMed Central  Google Scholar  Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119…

Continue Reading PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes

Calculate melting temperature for BLAST output (DNA duplexes with mismatches and gaps)

Calculate melting temperature for BLAST output (DNA duplexes with mismatches and gaps) 0 I know there are a lot of methods to estimate the Tm of a sequence with mismatches and gaps. I’ve been using biopython and getting negative values for the addition of gaps. I’m not sure if there…

Continue Reading Calculate melting temperature for BLAST output (DNA duplexes with mismatches and gaps)

Introduction to Biopython

The powerful bioinformatics programme Biopython has become a standard resource for experts in the area. You are given an introduction to Biopython in this article, which also covers its installation and provides examples that demonstrate its use. Even though we’re going into Biopython, remember that it’s only a small part…

Continue Reading Introduction to Biopython

Accepted python-biopython 1.81+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 10 Jul 2023 22:50:52 +0200 Source: python-biopython Architecture: source Version: 1.81+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 (1.81+dfsg-1) unstable; urgency=medium . * Migrate biopython 1.81 to unstable. * Merges fixes…

Continue Reading Accepted python-biopython 1.81+dfsg-1 (source) into unstable

Accepted python-biopython 1.80+dfsg-6 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 10 Jul 2023 22:27:12 +0200 Source: python-biopython Architecture: source Version: 1.80+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1040776 Changes: python-biopython (1.80+dfsg-6) unstable; urgency=medium . * d/control: depend on python3-reportlab (>= 4.0.4-1~)….

Continue Reading Accepted python-biopython 1.80+dfsg-6 (source) into unstable

Accepted python-biopython 1.80+dfsg-5 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sun, 09 Jul 2023 17:48:34 +0200 Source: python-biopython Architecture: source Version: 1.80+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: 1036174 1039565 Changes: python-biopython (1.80+dfsg-5) unstable; urgency=medium . [ Andreas Tille ] * Drop…

Continue Reading Accepted python-biopython 1.80+dfsg-5 (source) into unstable

Bug#1040776: python-biopython: autopkgtest regression

Source: python-biopython Version: 1.80+dfsg-5 Severity: serious ci.debian.net/data/autopkgtest/testing/amd64/p/python-biopython/35614880/log.gz … 580s ====================================================================== 580s ERROR: test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf) 580s Construct and draw PDF using method approach. 580s ———————————————————————- 580s Traceback (most recent call last): 580s File “/tmp/autopkgtest-lxc.aeaunhwi/downtmp/autopkgtest_tmp/Tests/test_GenomeDiagram.py”, line 1001, in test_diagram_via_methods_pdf 580s gdd.write(output_filename, “PDF”) 580s File “/usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py”, line 244, in write 580s return _write(self.drawing,…

Continue Reading Bug#1040776: python-biopython: autopkgtest regression

Remove sequences with (50% gaps) from MSA

Remove sequences with (50% gaps) from MSA 1 How do I remove sequences from my MSA that contain 50% gaps? I know there are various posts about removing columns with gaps. But I’m looking for a simple script to identify alignments within my MSA that have >50% gaps “-” and…

Continue Reading Remove sequences with (50% gaps) from MSA

Kaggle competition, enzyme stability prediction, machine learning in life sciences, protein engineering, ML6

When Christmas is nearing, everybody is looking forward to the Christmas tree, maybe snow, presents, Santa Claus and the new year. For us at ML6, there is something more! We get some time off our regular projects and get to spend time exploring new horizons for ML6: new tech, new…

Continue Reading Kaggle competition, enzyme stability prediction, machine learning in life sciences, protein engineering, ML6

FASTQ Phred33 average base quality score

FASTQ Phred33 average base quality score 2 I have a FASTQ dataset where I’m trying to find the average base quality score. I found this old link that helped somewhat (www.biostars.org/p/47751/). Here is my script (I’m trying to stick to awk, bioawk or python): bioawk -c fastx ‘{print “>”$name; print…

Continue Reading FASTQ Phred33 average base quality score

Working with mappy and comparing it to Blast

Working with mappy and comparing it to Blast 0 Hello! Following a previous post of mine (Alignment error using Biopython) and thanks to the kind help of @zorbax i came up with this piece of code to do the alignment i wanted: import mappy as mp import re # Load…

Continue Reading Working with mappy and comparing it to Blast

Alignment error using Biopython

Alignment error using Biopython 1 Hello, i am trying to write a program using biopython that will align some sequences from a fasta file (for the test that i will present 5 of them) against a fasta file containing a genome. For each, gene-genome alignment i want the score of…

Continue Reading Alignment error using Biopython

Dash Speck resets to default view state with Dash Loading States

Describe the bug Updating the view parameters from the presets results in no corresponding change in the component. To Reproduce Steps to reproduce the behavior: Change to the “View” tab Select “Use presets” Change atom style or rendering style Expected behavior Atom style or rendering style should change. Python version:…

Continue Reading Dash Speck resets to default view state with Dash Loading States

Bugs : python-reportlab package : Ubuntu

Removal request————— Please remove the old python3-renderpm & python3-reportlab-accel binaries built from src:python-reportlab for any architecture from Mantic. The binary packages are:python3-renderpm 3.6.13-1python3-reportlab-accel 3.6.13-1 Those binary packages got dropped by the Debian maintainer in 4.0.4-1https://bugs.debian.org/1037483 Additional information:A few reverse-depends are affected, which should be handled individually: $ reverse-depends python3-renderpm -r…

Continue Reading Bugs : python-reportlab package : Ubuntu

TCTTCTC) in a reference genome

Hello everyone, here’s my question: I would like to get all the genomic coordinates relative to a very small sequence (TCTTCTC) in a reference genome. I am aware that this would result in around 200,000 coordinates or so. I tried with blastn and with an alignent with bowtie/bwa, however the…

Continue Reading TCTTCTC) in a reference genome

MeiraGTx hiring Bioinformatics Analyst/Scientist I, Molecular and Protein Engineering in New York, New York, United States

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

Continue Reading MeiraGTx hiring Bioinformatics Analyst/Scientist I, Molecular and Protein Engineering in New York, New York, United States

Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Wang, Wei-Lin et al. Application of metagenomics in the human gut microbiome. World J. Gastroenterol. 21, 803–814 (2015). Article  ADS  PubMed  PubMed Central  Google Scholar  Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021). Article  CAS  PubMed  Google…

Continue Reading Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Need help using Biopython

Need help using Biopython 0 Hello, I am new to Biopython. But it shows up in my root folder in Anaconda on the website as well as lib/sitepackages however when I try something like this in Visual studio or PyCharm I get squiggly lines. I’ve deleted and reinstalled. I am…

Continue Reading Need help using Biopython

How does ncbi-blastP calculate the score ? (Why it is lower than mean-diagonal(blossum62) * length ) ?

Question briefly: Let is take an example of SRC human protein (P12931) – length 536 – on top of the blastP output we will see SRC itself – with score 1119 . Why ? What bothers me – diagonal of the blossum62 matrix – 4,5,6,9.. so in my mind output…

Continue Reading How does ncbi-blastP calculate the score ? (Why it is lower than mean-diagonal(blossum62) * length ) ?

Asking for feedback on a Python library for computing alignments

I want to point out another implementation that has Python bindings, parasail: github.com/jeffdaily/parasail Other comments Installation Information is severely lacking, I had to figure out myself what needs to be installed using mamba, it was quite annoying to get it to compile, the setup.py is not listing and reporting the…

Continue Reading Asking for feedback on a Python library for computing alignments

Getting Pairwise Sequence Alignment Score With Biopython

Getting Pairwise Sequence Alignment Score With Biopython 2 Hello, I used the following code to run clustalw.I got an alignment file using this code. But I need to get pairwise sequence alignment score and also has to get distance matrix based on sequence identity.My aim is to do hierarchical clustering….

Continue Reading Getting Pairwise Sequence Alignment Score With Biopython

Calculate Radius of Gyration [python 3]

Calculate Radius of Gyration [python 3] 0 Hello Everyone, I am trying to find a way to calculate the Rg (Radius of Gyration) of a protein. I searched through Biopython but I could not find a way to do it. Is it possible to do this calculation from Biopython? Is…

Continue Reading Calculate Radius of Gyration [python 3]

Bioinformatics Programmer II Job Opening in HOUSTON, TX at Texas Children’s Hospital

The Bioinformatics Programmer II works with limited supervision to formulate and define project scope and objectives through investigation and fact finding to develop or modify complex information systems handling biological data. He/she uses knowledge of molecular biology and computer science to manipulate and process complex data sets. Data management involves…

Continue Reading Bioinformatics Programmer II Job Opening in HOUSTON, TX at Texas Children’s Hospital

What are recommended parameters for the local protein alignment ?

Question: What are the recommended PARAMETERS for the local protein alignment and how important they are ? As far as I understand BLOSSUM62 is typical choice for the substitution matrix. Here in example below the params “opening gap penalty -4, extension penalty -1” are used – is it typical choice…

Continue Reading What are recommended parameters for the local protein alignment ?

Senior Scientist/ Scientist, Bioinformatics at Fate Therapeutics, Inc.

Fate Therapeutics is looking for a Senior Scientist or Scientist with expertise in bioinformatics to join the Molecular Engineering team.    The primary focus for this position will be to independently develop, optimize, and implement NGS pipelines to support advancement of Fate’s gene editing platform. The position will also establish, modify,…

Continue Reading Senior Scientist/ Scientist, Bioinformatics at Fate Therapeutics, Inc.

how to sort a fasta file

Using Python: This code reads your FASTA file, stores the entries in a dictionary and writes them back to a new FASTA file in a sorted order. It assumes that your FASTA file is formatted properly with each sequence header preceded by a “>”. from Bio import SeqIO # read…

Continue Reading how to sort a fasta file

convert fasta to fastq without quality score input file

Here’s another beginner BioPython question from me… I’m running some genome assemblies for someone who has some new Illumina sequence data and also had done some sequencing a few years ago. They have some Sanger and 454 sequences (a couple thousand sequences with a couple thousand base pairs for each)…

Continue Reading convert fasta to fastq without quality score input file

What Are The Most Common Stupid Mistakes In Bioinformatics?

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

Continue Reading What Are The Most Common Stupid Mistakes In Bioinformatics?

biopython – Why does my for loop in Python never stop running?

I am creating a code that takes accession numbers from an existing excel file and ultimately running it through BLAST using Entrez. I am very new to Python and pretty much just learning as a I write. Here is what my code looks like right now, it currently will run…

Continue Reading biopython – Why does my for loop in Python never stop running?

python – Unable to access individual alignment strings in biopython pairwise align

I’m trying to access individual strings in the alignment object which is produced by the pairwise aligner in biopython but not getting anywhere. I’m talking about the already aligned sequences showing gaps, as given by the print(alignment), but trying to get them individually or even slice. The documentation stipulates it’s…

Continue Reading python – Unable to access individual alignment strings in biopython pairwise align

python – BioPython – How do I allign multiple sequences at once?

(This may be a really stupid question, but I cannot find what I’m looking for in the documentation) I’m trying to align multiple sequences at once. From the biopython package, I can see how I can make an alignment of two sequences, e.g.: from Bio.Seq import Seq from Bio import…

Continue Reading python – BioPython – How do I allign multiple sequences at once?

Segmentation fault Biopython pairwise alignment

Segmentation fault Biopython pairwise alignment 0 Hi everybody ! I’m working in order to create my own pairwise sequence alignment program in Python. I use the pairwise2.align command from Bipython. When I use it with small sequences it works. I put the code bellow (2 for a match, -2 for…

Continue Reading Segmentation fault Biopython pairwise alignment

biopython – Trouble with data extraction and adding functions to formula in Python Pandas

enter image description here in the data frame a control group and two experimental groups, as well as 9 substrate concentrations, the question is how to properly extract this data and add features for further processing. this formula for calculating the average value =(B5+B6)/2-B4, and second formule my function =B7/60003,5/1000500/3/O87*1000000…

Continue Reading biopython – Trouble with data extraction and adding functions to formula in Python Pandas

‘position-aware’ aligning of sequences with letter annotations

I’ve been racking my brains about the best way to do this for a while now but am no closer to the answer it seems, so I could use some help! I’ll explain the problem conceptually, then in context as that may help. Essentially the problem is this: Given a…

Continue Reading ‘position-aware’ aligning of sequences with letter annotations

Arch Linux – python-biopython 1.81-2 (x86_64)

python-biopython 1.81-2 Architecture: x86_64 Repository: Extra Description: Freely available Python tools for computational molecular biology Upstream URL: www.biopython.org License(s): custom Maintainers: Filipe Laíns Package Size: 2.9 MB Installed Size: 17.5 MB Last Packager: Antonio Rojas Build Date: 2023-04-20 17:55 UTC Signed By: Antonio Rojas Signature Date: 2023-04-20 17:56 UTC Last Updated: 2023-05-19…

Continue Reading Arch Linux – python-biopython 1.81-2 (x86_64)

Problems going from biopython motif to logo

Problems going from biopython motif to logo 0 Hello, I’m trying to go from Bio.motif elements into logos and the available resources haven’t solved my particular problem. The motif.weblogo() function doesn’t seem to be working. There’s a previous issue asking about it, and I have the same problem, but none…

Continue Reading Problems going from biopython motif to logo

python – Using Biopython to the find the Isoelectric Point of proteins given an accession number

I have to complete a program that allows the user to get a list of proteins with a pI (isoelectric point). Below is a function given to me, and def calcChargeAtpH(sequence, pH=7.0): # calculate charge (pKa) ”’Calculate the net charge of a protein at a given pH”’ pK={# pK values…

Continue Reading python – Using Biopython to the find the Isoelectric Point of proteins given an accession number

Best way to obtain info from genbank given accession codes

Best way to obtain info from genbank given accession codes 1 Hi all, I have a lot of (order of a million) accession codes that I need to fetch info of from genbank. I have found these by blasting nucleotide sequences against the nt database. I’d like to know whether…

Continue Reading Best way to obtain info from genbank given accession codes

Biopython error: “ModuleNotFoundError: No module named ‘Bio.SubsMat'”

2 hours ago Alexander &utrif; 70 Making import I am getting such an error: from Bio.SubsMat import MatrixInfo “ModuleNotFoundError: No module named ‘Bio.SubsMat'” Would you be so kind to suggest something ? Googling does not seem to lead to the same error. PS Some time ago it was working okay,…

Continue Reading Biopython error: “ModuleNotFoundError: No module named ‘Bio.SubsMat'”

sequence analysis – How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?

This question was migrated from Biology Stack Exchange because it can be answered on Bioinformatics Stack Exchange.Migrated yesterday. 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…

Continue Reading sequence analysis – How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?