Tag: ClustalW

Epidemiology, genetic diversity, and association of canine circovirus infection in dogs with respiratory disease

Animal and ethics A total of 190 dogs, comprising both healthy dogs (n = 76) and dogs with respiratory symptoms (n = 114), were included in this study. The research assessed nasal swab (NS) and oropharyngeal swab (OS) collected between January and November 2020. The samples from the healthy group were collected from clinically…

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clustalw and muscle in Biopython

First, try installing Biopython 1.63 from here, it may solve some of your problems. Second, make sure you’re using the latest Python from python.org – you might want to run the installer again just to ensure that none of your files are corrupted, if you’re still getting the same error…

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Multiple Sequence and Clustalw Write Up

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BenchSci hiring Bioinformatics Engineer (Remote) in Toronto, Ontario, Canada

BenchSci’s vision is to bring novel medicine to patients 50% faster by 2025. We’re achieving it by empowering scientists with the world’s most advanced biomedical artificial intelligence. Backed by F-Prime, Gradient Ventures (Google’s AI fund), and Inovia Capital, our platform accelerates science at 15 top-20 pharmaceutical companies and over 4,300…

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What is ClustalW alignment?

ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools. How does protein alignment work? In typical usage, protein alignments use a substitution matrix to assign scores to amino-acid…

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ClustalW on Ubuntu – DevDreamz

The section is copied from the BioPython documentation. >>> from Bio.Align.Applications import ClustalwCommandline>>> cline = ClustalwCommandline(“clustalw2″, infile=”opuntia.fasta”)>>> print(cline) clustalw2 -infile=opuntia.fasta If you run from Bio.Align.Applications import ClustalwCommandline cline = ClustalwCommandline(“clustalw2″, infile=”opuntia.fasta”) print(cline) it will do 3 things Import ClustalwCommandline module from BioPython Create a ClustalwCommandline object Print the object’s string…

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What is ClustalW? Tutorial of How to Use ClustalW

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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Clustal Processing Massive Dataset

Hello wonderful beings of bioinformatics! I’m new to this world and could use some help. My job is to run multiple sequence alignment on a large dataset. I am looking into the L1 family of genes and wanting to compare 7,525 elements of full length sequences. Each sequence is ~6,000…

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Bioinformatics script using Python/Biopython/Clustalw using stdout to iterate over a directory of proteins

What exactly is the error you are seeing? You shouldn’t set sys.sterr and sys.stdout to string values (the clustalw_cline() function returns the clustal stderr and stdout as strings), as you won’t be able to write anything to stdout from python. I tried to clean up and correct your code below….

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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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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

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haplotype network analysis with Pegas package in R

Hi all, I am very new in haplotype analysis and have faced with some problems that I do not know how to solve. I want to generate haplotype networks for sodium channel (DKr gene) in anopheles species. I have converted my vcf into fast file, produced multiple alignment with ClustalW…

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