The description line (defline) or header line, which begins with '>', gives a name and/or a unique identifier for the sequence, and may also contain additional information. In a deprecated practice, the header line sometimes contained more than one header, separated by a ^A (Control-A) character.
In the original Pearson FASTA format, one or more comments, distinguished by a semi-colon at the beginning of the line, may occur after the header. Some databases and bioinformatics applications do not recognize these comments and follow the NCBI FASTA specification. An example of a multiple sequence FASTA file follows:
Campbell Ritchie wrote:Cannot see how encoding problems could cause nulls to be returned. If you look up the FASTA files they appear to contain ASCII characters only, so encoding problems are unlikely.
Since file input streams read bytes they are not suitable for reading text files. Java® Tutorials link. OP says clearly it is a text file he is reading.
Sounds unlikely to me. It is because he is only reading every other line
Liutauras Vilda wrote: . . .
Maybe the nulls is being returned because those omitted parts are written only in 5 lines in a raw file, and length is ~ 3000 symbols per line (might this is a case)
That will not give a null line but a, empty String like "".
And 2 empty lines at the end of file with "carriage return followed by a line feed" tags (it explains why at the end he gets null received)