[Biojava-l] (no subject)

[piroska.devay at pharma.novartis.com]

Dear All,

I am new to biojava and unfortunately new to Java also.
Parsing a Fasta output I could modify the FastaSearchSAX Parser to return 
the parsed data on the standard output.
In the Fasta output the query-hit alignments are not returned, instead the 
query sequence and the subject sequence are returned separately.
If the sequences were shifted by Fasta for matching, '-' symbols are 
inserted 
(-----------------------QVQLQQSGNELAKPGASMKMSCRASGYSFTSYWIHWLKQRPDQGLEWIGYIDPATAYTESNQKFKDKAILTADRS)
I would like to align these sequence-strings. I simply would have 2 
strings as an input or converted into  SymbolLists.
I don't seem to find the right class to do this. 
Could someone offer advice or refer me to some sample programs that I can 
browse through or a more detailed tutorial?

Thanks very much,

Piroska