Re: Removing nucleotide frm sequence

[space_monk]

You probably want something more refined than this, but something similar to:

while (<>) {
    # $ denotes end of string
    s/AAAAA$//;
    s/>CC\@B$//;
    print;
}

Not quite sure if your sequence is on one line or multiple lines, so the above will need some tweaking. If you need some more help, please amend your question, putting a complete sequence in code blocks

[bingalee]

Hey, thanks for that..but the quality and the last five nucleotides aren't the same in every sequence. It can also be like AAACT in another sequence..:(

[space_monk]

Please can you put a complete sequence or two in the comment, with a short explanation of what needs removing. Many of us aren't chemists (I only got a low grade at Chem A level 30 years ago :-)

[space_monk]

local $/ = "";
while (<>) {
    # should have a whole record
    # split up 4 line record
    my (@line) = split( "\n");
    # change if necessary to check we have a valid record
    if ($line[0] =~ /^@/) {
       $line[1] =~ s/([ACGT]{5})$//;
       $line[3] =~ s/(\w{5})$//;
       print join("\n", @line);
    }
}