Welcome to Biojava! to get data from NCBI I reccomend using their eutils (http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html)
to read sequence text files (or the sequence text returned by NCBI) have a look at the tutorials about SeqIO on http://www.biojava.org/docs/bj_in_anger/index.htm to interact with a SQL database I would reccomend getting a very recent version of biojava from CVS and a very recent version of BioSQL (http://obda.open-bio.org/) from the open-bio cvs server (http://cvs.open-bio.org/) the have a look at the BioSQL tutorials at the bottom of the Biojava in Anger page (http://www.biojava.org/docs/bj_in_anger/index.htm) Keep posted for updates on the biojava / biosql interface. This is an area of active development. Best of luck. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Simon Moses <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 05/11/2005 05:22 PM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] accessing data in servers(ex. NCBI) from our java programmes dear sir, i am new to biojava. i want to access data from NCBI(or other Databanks) with my programme. is there any possibility to send a 'select query' and get data? how to know the format in which the data is stored? like textfile, oracle database, mysql etc.. if data is stored in any RDBMS what is the connection string? if data is in textfiles how to know the path and file names? are the paths are fixed? my intention is to send an sql query, get data, process it and display in my programme after checking few conditions. i have seen an application which runs in client machine and accesses these databases. for example, if we give our DNA in that programme and select the server and database, programme will search in NCBI server and give DNA sequences which are nealy equal. thanks in advance --Simon Moses ************************** Visit My Home Page http://www.geocities.com/ks_moses updated: 28 Sep 2004. Simon Moses ************************** --------------------------------- Yahoo! Mail Stay connected, organized, and protected. Take the tour _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
