search for: aacttttttttaaa

...those lines have to be extracted if the patterns at the beginning of the line. Example with matching line 1, non matching line 2, non-matching line 3 (line three comprises aaa, but not at the beginning of the line 3): SearchPattern = "^aaa" Text file: aaaooooooooooo bbbiiiiiiiiiii aacttttttttaaa Going line by line through the file in R is too slow, and I cannot program it in C or C++. Hence I use the fgrep command. I would appreciate if anyone has a fast alternative which works with R on Linux and Windows systems.