Category: Biopython

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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Apparently random fluctuations in coverage via CodeCov?

I would need to go back over some (ideally merged) pull requests to check, but my strong impression compared to when we ran TravisCI/CircleCI/AppVeyor to now with GitHub Actions/CircleCI/AppVeyor, the unit test coverage reported via CodeCov is much more random. So, it that really the case? If so, how can…

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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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Getting cDNA sequence from NCBI

Getting cDNA sequence from NCBI 1 I am looking at NCBI’s api page and I cannot seem to find any endpoint that returns the cDNA by transcript id. In fact NCBI nuccore has a webpage for this. and if I want to i can scrape the part coming after ORIGIN….

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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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How can i get sequences from a big list of accession number from NCBI?

How can i get sequences from a big list of accession number from NCBI? 1 Hi, everyone! I’m new to this world and im getting acquainted to Biopython.. is there a way on biopython to retrieve the sequences from a txt file with several accession numbers? gene NCBI Biopython •…

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Plotting PCA chart using biopython

Hi, Im trying to plot a PCA chart using biopython. I’m new to biopython and python in general so excuse me if my code doesnt look good. I tried to do something like that: from Bio.Cluster import pca import numpy as np import pandas as pd import matplotlib.pyplot as plt…

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How to get accession number on NCBI and how to get their gene sequences?

How to get accession number on NCBI and how to get their gene sequences? 0 Hi, everyone! I’m new to this world and im getting acquainted to Biopython.. On NCBI I did >> specie 1(organism) OR specie2(organism) OR specie3(organism) OR.. AND (gene1 OR gene2) Which from that i donwloaded the…

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Filtering MSA by similiarity to a consensus sequence/motif

Filtering MSA by similiarity to a consensus sequence/motif 0 Dear all, anyone knows a good way of filtering or sorting a large multiple sequence alignment (~8000 sequences) by similarity to a given consensus sequence? A solution using python/biopython would be optimal. Any help is appreciated! Best Jonathan biopython motif multiple…

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