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 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
