Really I'm only interested in the gaps that occur at the beginning of the sequences. For example:Īlignment$shift <- str_count(alignment$Sequence, "-")īut this fails me when I have gaps downstream in my sequence. So far I've tried using the str_count function. What I want to do is read through my data frame and count how many spaces are at the beginning of each sequence. "-NIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNVDRWLATILIEPNVQATNRTYNLFGQQEILLIENTSQTQWKFVDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNVT-TGY-YSTTNYDTVNMT-"))Įach of the dashes represents a space. "MASLIYRQLLTNSYTVNLSDEIQNIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTAEGVVIQGTNNTDRWLATILIEPNVQATNRTYNLFGQQETLLVENTSQTQWKFVDVSKTTSTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNAA-TGY-YSTTSYDTVNMTSSCDFYIIPRSQEGKCTEYINYGLPPIQNTRNVVPVALSAREIVHTRAQVNEDIVVSKTSLWKEMQYNRDITIRFKFDRTIIKAGGLGYKWSEISFKPITYQYTYTRDGEQITAHTTCSVNGVNNFSYNGGSLPTDFAIS-", "Sequence" = c("MASLIYRQLLTNSYTVNLSDEIQNIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTAEGVVIQGTNNTDRWLATILIEPNVQATNRTYNLFGQQETLLVENTSQTQWKFVDVSKTTSTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNAA-TGY-YSTTSYDTVNMTSSCDFYIIPRSQEGKCTEYINYGLPPIQNTRNVVPVALSAREIVHTRAQVNEDIVVSKTSLWKEMQYNRDITIRFKFDRTIIKAGGLGYKWSEISFKPITYQYTYTRDGEQITAHTTCSVNGVNNFSYNGGSL-", My alignment can be read in as a data frame. I am analyzing an alignment of amino acid sequences using R and need a reproducible way to figure out where the start is for each sequence.
0 Comments
Leave a Reply. |