I have a simple, but tricky question: I have created a txt file containing several sequences representing a single gene from 20 species, each sequence starts like a fasta file (with > at begining). Now I have saved this as a (.fas ) file using Bioedit software. I want to rund multiple alignment and phylogenetic analyses in R on these sequences. I have used the read.fasta function but gave me an error. I used this : '''sequence
Hi Mohamed Samir
I think the read.fasta should work. Please provide a sample input to examine or at least the error message you encountered. It would be really hard to diagnose the problem without that. Thanks.
Hi,Mohamed Samir:
It's my honor to help you. I think the 'Biostrings' toolbox can be used in your research!
You can refer to the following Web adress:
https://bioconductor.org/packages/release/bioc/html/Biostrings.html;
http://www.bioconductor.org/packages/release/bioc/manuals/Biostrings/man/Biostrings.pdf
Thanks!
Dear Sahu,
This is an example txt file. The idea is to convert this to fasta file, which I can then readnit in R. It contains 3- sequences from 3 species ...
Dear Mohamed Samir
The problem is with the input file. A proper fast file must have the > symbol or else it throws an error. Simply put > symbols at the beginning of the sequence identifiers without any spaces between them. Furthermore, my suggestion is always to save a fasta file as a .fasta or .fas file. Thanks
Dear Mohamed Samir,
Yes you can use the readDNAStringSet() function from the Biostrings package in R. To this command you can give the text file file containing the multiple sequences and specify fasta format. Ex: sequence
I've also had problems with this...I just didn't use all the arguments and then my file was read well.
i.e., I used: read.fasta("Sequences1.fas"), or read.fasta("Sequences1.fasta") in my case because I saved it in .fasta, instead of: read.fasta(file = "Sequences1.fas", seqtype = "AA", as.string = TRUE, set.attributes = FALSE)
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