Tag: ClustalO

MAFFT benchmark

Benchmark dataset The following datasets, HomFam and OXFam were used as benchamrk datasets in “Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees”. HomFam This HomFam dataset is modified version of original HomFam dataset constructed by the authors of Clustal…

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Clustalo failing to complete multiple sequence alignments

Clustalo failing to complete multiple sequence alignments 0 Hi, I have been using clustalo in the terminal to create multiple sequence alignments for the past few weeks, but every time I try lately it fails. I’ve tried on two computers, with different files. I’ve tried looking up the errors but…

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Change Residue Output Length in trimAl?

Change Residue Output Length in trimAl? 0 Hello, I am looking for a way to change the length of the residues printed in the output of trimAl. Using clustalo, I have generated .aln data that looks like so: chr1_38402816-38409352 ———————————————————————————agatcatgaacttttgctc–ca—agaactattgcaggaa-cataccagga-aagccgagagaatccacagaccctttgaaggaagtggatt chr1_41176265-41182362 ——————————————————————————————————————————————————————————- chr1_42059276-42065372 ——————————————————————————————————————————————————————————- I was able to see 175…

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comparing and aligning two sequences to spot protein level differences using Expasy / Uniprot clustalO : bioinformatics

Hi there, confused student. I’ve been using expasy translate to convert two nucleotide sequences into protein where I can then see open reading frames. By then using uniprot clustalO I hoped to paste the open reading frames for both sequences and align them to spot any differences between the two….

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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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ClustalO with multithreading parameter threads appear sleeping

ClustalO with multithreading parameter threads appear sleeping 0 Hello folks, I am running clustalo with threads flag, at the begining clustalo was using the number of threads I specified but when I checked it next day, all of the threads seem sleeping except one. Do you think thats normal, or…

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