[Biojava-l] Money For the Painfully Shy

* DEFINITELY HAPPY SMOKING! * MOOD ENHANCER * SMOKEABLE / BREWABLE MOOD FOOD!! * GOOD-BYE STRESS. * GOOD-BYE ANXIETY. * GOOD-BYE RESTLESSNESS. * SLEEP DEEP! * GOOD-BYE FUNKY DREAMS! * YOU’LL BE GLEAMIN DREAMIN. * HORNIER THAN HORNY GOATWEED!!! * SUPERLATIVE MIXER WIT

[Biojava-l] Re: Question about Swiss-Prot parsing

> Has anyone found workarounds for these. There are several specialized (non-BioJava) parsers for Swiss-Prot if you need more detailed information than available through the BioJava model. Let me know if you are interested... -- Eric Jain ___ Bioj

[Biojava-l] how to calculate consensus from a fasta file

fasta file and get all the sequences. Let's consider the sequences as lines. I'd like to calculate the column consensus using dna degenerate alphabet. Does biojava implements a way to do this? Thanks by advance. Eric __ Do you Yahoo!? Yahoo! Hotjobs

Re: [Biojava-l] how to calculate consensus from a fasta file

ry... Anyway thanks for your help. Eric --- [EMAIL PROTECTED] wrote: > Hi Eric - > > I'm not sure if this will solve your problem but you > could make an > Alignment object from the sequences and then use the > methods of > DistributionTools to get a Distribution

[Biojava-l] ClassCastException during ambiguity calcul

ion must be thrown during this code execution, I don't think the class cast exception is the good one. Does someone have a clue? Is it a bug? Do you want me to propose a fix? I think I got good java skills but the worst biological skill you've ever seen :-) Regards, Eric __

[Biojava-l] is valid character

first like to remove (or replace) all of the invalid characters. Eric Buckley ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] Biotechnology group?

hways satellite workshop at ISMB in Copenhagen this July, but details still need to be worked out. Eric _ Eric Neumann, PhD VP Bioinformatics Beyond Genomics www.beyondgenomics.com tel: 617-497-2233 fax: 617-497-2244 _ "Wiepert,

Re: [Biojava-l] any books on biojava

ou edit the new page. When that new page has some content, the question mark on the other page will go away. Wiki is very concerned with connectedness. Hence, the normal way to create a new page (or topic) is to refer to it first. cheers, Eric Blossom mailto:[EMAIL PROTECTED] Blossom

Wiki Book (was Re: [Biojava-l] any books on biojava)

Take a look at http://www.leuf.net/wiki/files/WikiWay_04.pdf for a sample chapter of the book I mentioned. Eric Blossom mailto:[EMAIL PROTECTED] Blossom Associates West http://www.BlossomAssociates.Com/ 510 841-3338

RE: [Biojava-l] FramedFeature interface

external formats as well as letting a user choose a numbering style in a GUI. This might allow some flexibility and promote the reuse of packages that are not bio-oriented. Many of these use 0 based numbering. cheers, Eric Blossom On Wed, 5 Sep 2001, Mark Schreiber wrote: > On Tue, 4 Sep 2

[Biojava-l] LocationTools.buildLoc

Is there any reason for the org.biojava.bio.symbol.LocationTools.buildLoc method to be protected rather than public? -- Eric Jain ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] LocationTools.buildLoc

ation makeContigiousLocation(int min, int max); Sounds a bit like makeContagiousLocation, but whatever... -- Eric Jain ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] GMANE

Would be nice if this mailing list were registered with http://www.gmane.org/. Just for the people who prefer news servers over mailing lists... And BioPython is there already :-) -- Eric Jain ___ Biojava-l mailing list - [EMAIL PROTECTED] http

[Biojava-l] Re: Running apps with Java

problematic command line applications can be made to fail reproducibly, using Java 1.4. -- Eric Jain ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] Re: Biosql performance numbers?

ueries into the database, and keeping the actual entries in indexed text files. -- Eric Jain ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] [Biojava-dev] Java 1.5 (final chance to object)

balk at the cost of upgrading to Java 1.5 (both the JVM and the application server). Thanks. -Eric Trull ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] help on blast

p://www.ncbi.nlm.nih.gov/BLAST/developer.shtml for documentation and a Perl example. Good luck! -Eric Trull --- Francois Pepin fpepin at cs.mcgill.ca wrote: > Hi Parveen, > > This might not be as easy as you might like. > > The applet runs on the client, so you need the applet t

[Biojava-l] SAXException with BLAST errors

ESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNL #-- Thanks. -Eric Trull ___ Biojava-l mailing list - Biojava-l@b

Re: [Biojava-l] SAXException with BLAST errors

No, I use BioJava to write the user's query sequence as a fasta file before feeding it to BLAST. I just copied a differently formatted sequence into my post. Thanks. -Eric Trull --- [EMAIL PROTECTED] wrote: > Not exactly sure what the problem is here but it looks like your input is

Re: [Biojava-l] SAXException with BLAST errors

that it has a chain 'e' and a chain 'E'. When I created my FASTA file to feed to formatdb I made the deflines of the form pdb||, but in uppercase. So I had two entries with the same defline but different sequences. I think this is my problem and am working on fixing it n