Python Programming for Biology: Bioinformatics and Beyond

Reading FASTA files

The FASTA text format is used to store nucleotide or protein sequences, using one-letter

codes (as illustrated in Figure 6.4). Each file can store one or more sequence entries. An

individual sequence entry spans two or more lines: the first line is a textual comment or

identifier  for  the  sequence  (e.g.  a  gene  or  protein  name  with  database  codes),  and  the

remaining  lines  contain  the  sequence  of  residue  codes.  The  first  comment  line  for  each

sequence  begins  with  the  ‘>’  character.  (Originally  the  semicolon  character  ‘;’  was  also

allowed at the beginning of a line to indicate a comment, but that is no longer commonly

used.) Each line subsequent to the comment line contains part of the sequence, until either

the end of the file is reached or the next comment line occurs, indicating the start of the

next sequence. The lines of residue codes are normally no more than 60 characters long,

each character representing one nucleotide or amino acid in the sequence.