Hi, Try: Lines1 <- readLines(textConnection(">contig number 11 tttgctcggaggggatc >contig number 23 gaaaacacttccttattatacaggtaaaccgtatttggat >contig number 3 aaagctcggaggggatcccct")) seq1 <- "nnnnncattccattcattaattaattaatgaatgaatgnnnnn" concatenated_contig <- paste(Lines1[!grepl(">",Lines1)],collapse=seq1) concatenated_contig #[1] #"tttgctcggaggggatcnnnnncattccattcattaattaattaatgaatgaatgnnnnngaaaacacttccttattatacaggtaaaccgtatttggatnnnnncattccattcattaattaattaatgaatgaatgnnnnnaaagctcggaggggatcccct" A.K. Hi all, I have a sequence files with huge number of contigs such as (contig number does not reflect the order): >contig number 11 tttgctcggaggggatc >contig number 23 gaaaacacttccttattatacaggtaaaccgtatttggat >contig number 3 aaagctcggaggggatcccct ... .. I want to concatenate the contigs such that the above order is preserved, and also, I want to insert the sequence "nnnnncattccattcattaattaattaatgaatgaatgnnnnn" in each contig boundaries (here are two contig boundaries), such that the final output file would become as follows: >concatenated contig tttgctcggaggggatcnnnnncattccattcattaattaattaatgaatgaatgnnnnngaaaacacttccttattatacaggtaaaccgtatttggatnnnnncattccattcattaattaattaatgaatgaatgnnnnnaaagctcggaggggatcccct Any help in solving the problem is highly appreciated. Thanks in advance.. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.