[Biojava-l] (no subject)

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Mon Jan 17 21:34:56 EST 2005

Hi -

I'm not too clear on what you are trying to do but you may find the Blast 
and Fasta tutorials on this page helpful 
http://www.biojava.org/docs/bj_in_anger/index.htm Much of the stuff that 
is from the blast tutorials is relevant to the Fasta parsers.

>From my understanding of your email you are not getting some of the 
information you want from the standard classes. You should know that the 
SearchContentAdapters provided with BioJava do not capture every detail of 
a search, only the bits we thought were most interesting. If you need to 
get more (or less) information you will need to make a custom 
SearchContentAdapter (usually you just extend the SearchContentAdapter and 
override some or all of the methods).  Particularly you may want to look 
at http://www.biojava.org/docs/bj_in_anger/blastecho.htm which shows how 
to echo events from a BlastLikeSAXParser to STDOUT. It should be very easy 
to change this to echo for a FastaSearchSAXParser. Running this program 
will help you determine where the things you are looking for may end up 
and help you decide if and how you need to make a custom 
SearchContentAdapter to get the information you want.

Hope this helps,


Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670

phone +65 6722 2973
fax  +65 6722 2910

Piroska Devay/PH/Novartis at PH
Sent by: biojava-l-bounces at portal.open-bio.org
01/17/2005 11:53 PM

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] (no subject)

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 
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,

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