Tag: ClustalO

Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal

Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…

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Index of /~psgendb/birchhomedir/local/pkg/ugene/data/cmdline

Name Last modified Size Description Parent Directory   –   align-clustalo.uwl 2019-09-24 01:05 3.0K   align-clustalw.uwl 2019-09-24 01:05 5.1K   align-kalign.uwl 2019-09-24 01:05 2.8K   align-mafft.uwl 2019-09-24 01:05 2.7K   align-tcoffee.uwl 2019-09-24 01:05 3.1K   align-to-reference.uwl 2019-09-24 01:05 3.1K   align.uwl 2019-09-24 01:05 2.7K   convert-msa.uwl 2019-09-24 01:05 1.4K  …

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Clustal omega does not align: Killedssive alignment output

Clustal omega does not align: Killedssive alignment output 0 I have launched clustal omega from temrinal to align two sequences container din the file multi_seq.fa. However, I don’t get any output. It looks to me that clustal has stopped aligning: $ clustalo -i multi_seq.fa -o aligned_file_o.fa –outfmt=fa -v –force Using…

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Multiple sequence aligments – parallelisation

Multiple sequence aligments – parallelisation 1 I have a folder with approx 3.000 fasta files. Each fasta FILE corresponds to one gene (orthogroup) and it contains multiple sequences (orthologues from multiple species). I want to do multiple sequence alignments in ClustalO or MUSCLE for each of these files (genes). I…

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Plotting multiple sequence alignments from tblastn

I’m trying to visualize multiple sequence alignments (MSAs) of tblastn. My query was a protein sequence, against a genome with no proteome available. The output JSON from tblastn shows: “hits”: [ { “num”: 1, “description”: [ { “id”: “gnl|BL_ORD_ID|29”, “accession”: “29”, “title”: “LSRD01000030.1 Fusarium sambucinum strain F-4 contig00030, whole genome…

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How to get image of mutliple alignment sequence that is labeled by row?

I have been looking at many, many different multiple sequence alignment software packages. There’s a post that I was using earlier from BioStars, but I can’t find it anymore. ADOMA doesn’t produce anything. There is no error message, just blank HTML ESPript, which requires faxing or snail-mailing a license request,…

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The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

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How to use the clustal omega command line tool with custom gap penalty?

How to use the clustal omega command line tool with custom gap penalty? 0 Hi all, I compiled clustal omega (1.2.4) on my laptop and I can use it to align sequences by doing: clustalo -i sequences.fasta -o output.fasta in the terminal. I have checked both the help and the…

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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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