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newbie, again. I'm trying to run a msa using ggmsa. All sequences are short and simple, yet I'm still trying to figure out errors. Here's the problem (btw, don't judge me on my coding cause I know how bad I am in this, lol)

galanin_table <- c("MACSKHLVLFLTILLSLAETPDSAPAHRGRGGWTLNSAGYLLGPVLHLSSKANQGRKTDSALEILDLWKAIDGLPYSRSPRMTKRSMGETFVKPRTGDLRIVDKNVPDEEATLNL", "Rat", "MHRCVGGVCVSLIVCAFLTETLGMVIAAKEKRGWTLNSAGYLLGPRRIDHLIQIKDTPSARGREDLLGQYAIDSHRSLSDKHGLAGKREMPLDEDFKTGALRIADEDVVHTIIDFLSYLKLKEIGALDSLPSSLTSEEISQP", "Zebrafish", "MQRSFAVFCVSLIFCATLSETIGLVIAAKEKRGWTLNSAGYLLGPRRIDHLIQIKDSPSARGRDELVNQYGIDGHRTLGDKAGLAGKRDMAQEDDVRTGPLRIGDEDIIHTVIDFLSYLKLKEMGALDSLPSPLTSDELANP", "Pupfish", "GWTLNSAGYLLGPPPGFSPFR","M35", "WTLNSAGYLLGPEHPPPALALA","M871")

galanin_matrix <- matrix(galanin_table, byrow=T, nrow=5)
galanin_table <- as.data.frame(galanin_matrix, stringsAsFactors = F)
colnames(galanin_table) <- c("Sequences", "Species")
galanin_table <- as.data.frame(galanin_table)
galanin_list <- as.list(galanin_table)
galanin_asvector <- as.vector(galanin_list)
names (galanin_vector) <- names (galanin_list)
galanin_vector_ss <- Biostrings::AAStringSet(galanin_vector)
galanin_msa <- msa(galanin_vector_ss)
class(galanin_msa) <- "AAMultipleAlignment"

ggmsa(galanin_msa)

Updated: Oct 27, 2022, This is the new comment (and script) without the warning messages- yet still got 2 out of 5 sequences aligned.

sometimespetisometimesfeña
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  • Those are 'warnings', not 'errors', but I don't have `msa` installed, yet. And BioManager wants to help me 'get up to date', so this might take a while, considering the number of packages. Are you getting MSA figures in spite of the warnings? – Chris Oct 27 '22 at 14:19
  • Hi Chris- thanks for the clarification. I've improve the script and got rid of the warnings, yet I'm getting a msa figure with only 2 of the 5 sequences aligned. I think I'm getting there... gradually. I'm sharing the new one in case you want to check it. Thanks! – sometimespetisometimesfeña Oct 27 '22 at 17:30
  • Assuming a) I know nothing, b) is this a simple test where it is known that a given sub-sequence really is embedded in all sequences (i.e. Rat, zebrafish, pupfish & etc) and c) what the sub-sequence is? – Chris Oct 27 '22 at 18:01
  • I don't know the sub-sequence that should be present in all the others. I think I can run the test on ClustalW website and I'm just making my life hard cause I want to but still thought this will be a good exercise for me to start doing msa. The whole idea of the exercise is that I have two synthetic peptides (M35 and M871) that I want to match with biological peptides in other organisms (in rat, zebrafish, and pupfish) and know "where" they are matching identities – sometimespetisometimesfeña Oct 27 '22 at 18:55

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