Need a key for "paste" command

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http://www.unix.com – Is there a way to use the "paste" command to combine files and have each line key off of a column? All this time I've been pasting files together and foolishly not checking the line count of each file. I have just found out that the line count is not the same for each file so the data is not being synchronised properly across the two files. I'd like to avoid using a for loop to grep one line of each file, and the key in that file, against each line of the correlating file as the files are large and would increase the overhead. Anyway I can tell paste to match lines that have a co (HowTos)