User: reubenmcgregor88

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Posts by reubenmcgregor88

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How to get sequence homology percent from a multiple sequence alignment in DECIPHER?
... I have recently carried out a stipple sequence alignment using DECIPHER package in R. The code was fairly simple as follows: bod_aa <- readAAStringSet("BOD_aa.fasta") aligned_aa <- AlignSeqs(bod_aa) BrowseSeqs(aligned_aa) This worked nicely but I would like some information on the alignmen ...
decipher R protein alignment written 4 months ago by reubenmcgregor880
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Comment: C: How to combine sequences from different stringsets?
... Strange, I did try something similar and it combined the DNA from all the selected sequences into one long string, but I can not remember how I managed that. Thanks for this answer ...
written 7 months ago by reubenmcgregor880
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How to combine sequences from different stringsets?
... I have imported 2 sets of sequences in fasta format and imported them as DNAStringSets using decipher (which I believe uses biostrings for the basic manipulation of nucleic acts string sets): > extraemm_DNA_untrim1 A DNAStringSet instance of length 5     width seq                               ...
biostrings decipher written 7 months ago by reubenmcgregor880 • updated 7 months ago by Mike Smith2.9k
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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... Yes this has now worked,  I now have a slight issue that when I run the loop I get the error: Error in AlignSeqs(combAA) : At least two sequences are required. There are some sequences in the "allemmAA" that are nor present in my list of sequences, and I am guessing the error is coming from there ...
written 8 months ago by reubenmcgregor880
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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... Ah yes, I had a bit of code further down my R script re-assinging the "seq" variable. I re -ran as above and now get the error: Error in unlist_list_of_XVectorList(class(x), args, use.names = FALSE,  :    all elements in 'x' must be AAStringSet objects (or NULLs) As mentioned above I got the AAStr ...
written 8 months ago by reubenmcgregor880
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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... Thank you Erik, as always this is a very comprehensive and useful answer, and I can see I will have to get familiar with this kind of looping in order to cut down on time. Whilst I can see in theory what you are suggesting whenever I run the code: combAA <- c(allemmAA[1], seq[w])  I get the er ...
written 8 months ago by reubenmcgregor880
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Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... Background: I have in a fasta file with reference sequences for strains of bacteria and I want to align sequences I have from another source, in a data frame, to their corresponding reference sequences in the fasta. I know in theory I could put them all in the same file (fasta or data frame) but wo ...
biostrings decipher R written 8 months ago by reubenmcgregor880 • updated 8 months ago by Erik Wright130
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Comment: C: Is it possible to import many .tsr sequence file into R using bio strings for us
... Thought this might be the case, I think that may be beyond my capabilities but I will look into it. Thanks ...
written 8 months ago by reubenmcgregor880
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Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
... There are a series of amino acid sequences I want to import into R for alignment ,using DECIPHER, with some sequences I imported as FASTA sequences.  The ftp site I want to get them from is : ftp://ftp.cdc.gov/pub/infectious_diseases/biotech/tstransl/. Within this folder there are two types of file ...
biostrings decipher R written 8 months ago by reubenmcgregor880
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Comment: C: Colour a phylogenetic tree, based on column in DECIPHER?
... Yes subsetting seems to be the easiest way to do it, Is there a way to save the image opened in the web browser when using: BrowseSeqs(), rather than doing each strain iteratively and browsing one by one? ...
written 8 months ago by reubenmcgregor880

Latest awards to reubenmcgregor88

Scholar 13 months ago, created an answer that has been accepted. For A: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package

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