The first line in a FASTA file starts either with a ">"(greater- than) symbol or a ";" (semicolon) and was taken as a comment. Subsequent lines starting with a semicolon would be ignored by software. Since the only comment used was the first,it quickly became used to hold a summary description of the sequence, often starting with a unique library accession number, and with time it has become commonplace use to always use ">" for the first line and to not use ";" comments (which would otherwise be ignored).

Following the initial line (used for a unique description of the sequence) is the actual sequence itself in standard one-letter code. Anything other than a valid code would be ignored (including spaces, tabulators, asterisks, etc...). Originally it was also common to end the sequence with an "*" (asterisk) character (in analogy with use in PIR formatted sequences) and, for the same reason, to leave a blank line between the description and the sequence.

Example like:

>sp|P35680|HNF1B_HUMAN Hepatocyte nuclear factor 1-beta OS=Homo sapiens
MVSKLTSLQQELLSALLSSGVTKEVLVQALEELLPSPNFGVKLETLPLSPGSGAEPDTKP
VFHTLTNGHAKGRLSGDEGSEDGDDYDTPPILKELQALNTEEAAEQRAEVDRMLSEDPWR
AAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREIL
RQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGP
ASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWF
ANRRKEEAFRQKLAMDAYSSNQTHSLNPLLSHGSPHHQPSSSPPNKLSGVRYSQQGNNEI
TSSSTISHHGNSAMVTSQSVLQQVSPASLDPGHNLLSPDGKMISVSGGGLPPVSTLTNIH
SLSHHNPQQSQNLIMTPLSGVMAIAQSLNTSQAQSVPVINSVAGSLAALQPVQFSQQLHS
PHQQPLMQQSPGSHMAQQPFMAAVTQLQNSHMYAHKQEPPQYSHTSRFPSAMVVTDTSSI
STLTNMSSSKQCPLQAW