# Sequence file format

Various MEME Suite programs require as input a file containing protein or DNA sequences. These input files must be in FASTA format. The format is very simple. Every entry consists of a sequence identifier (ID), an optional comment (COMMENT), and a sequence (SEQUENCE). The format looks like this:

            >ID COMMENT
            SEQUENCE

The special character ">" marks the beginning of a new sequence. The ">" character is followed immediately by the sequence identifier. The rest of that line is occupied by the optional comment. Subsequent lines contain the sequence itself.

Some rules about representing sequences:

- Case doesn't matter. MEME Suite converts everything to uppercase.
- White space (spaces and newlines) within the sequence are ignored.
- Characters should be from a valid alphabet

Here is an example of three sequences in FASTA format:

          >ICYA_MANSE
          GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY
          DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN
          LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
          NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH

          >LACB_BOVIN
          MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA
          QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI
          DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
          KFDKALKALPMHIRLSFNPTQLEEQCHI

          >BBP_PIEBR
          NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE
          GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN
          VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
          GSPVVDSQKLVYSDFSEAACKVN