Re: [Biojava-l] Problem: Hibernate - RichSequence Annotation

abase from previous testing that may need cleaning out (although if the hibernate mapping is correct this is not likely). - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/09/2006 02:08 AM To: [email protected] cc: (bcc: Mark Schre

Re: [Biojava-l] BiojavaX EmblFormat

The biojavax parser uses regular expressions to parse these lines. I will need to check what needs changing in these regex's to allow parsing of these files. Thanks for your testing! - Mark "Jolyon Holdstock" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/08/2006 0

Re: [Biojava-l] odds ratio

y to be in the null >distribution, or am I doing something totally wrong here? If you used an odds scoring function then you have done things correctly. Sounds wierd. - Mark ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] problems with SubIntegerAlphabet

Fixed in CVS now - Mark "Heather Kent" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/02/2006 05:15 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] problems with SubIntegerAlphabet Hi

Re: [Biojava-l] problems with SubIntegerAlphabet

leSymbolList's .seqString() method as an example you can do the equivalent operation "manually" as a work around using "token" instead of default. Let me know if you have problems... I will also fix this bug in CVS shortly. - Mark "Heather Kent" <[E

Re: [Biojava-l] BioJavaX docbook minor corrections

this to you setDescription suggestion. - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/24/2006 08:53 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] BioJavaX docbook minor corre

Re: [Biojava-l] BioSQLRichSequenceDB: initialisation error

Hi - This should be resolved in CVS now. Let me know if it doesn't work. Best regards, - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/21/2006 01:34 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis)

Re: [Biojava-l] BioSQLRichSequenceDB: initialisation error

. - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/21/2006 01:34 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] BioSQLRichSequenceDB: initialisation error Hello, in the construc

[Biojava-l] last call for logos

Hello - Last chance to post a logo for the biojava logo (http://biojava.open-bio.org/wiki/BioJava:Logo). If you like one of the ones you see but think it could be improved why not modify it. This is open-source after all. "Voting" will start soon

[Biojava-l] release plan

. Let me know if you can help at all with any of the tasks. - Mark Mark Schreiber Research Investigator (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

[Biojava-l] RichAnnotation

= note.getValue(); The term has a name which is also a String String name = term.getName(); So to get the name, value pair of a note you would do this: String name = note.getTerm().getName(); String value = note.getValue(); Which is pretty much what the Note toString() method does. - Mark Mark

Re: [Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation

s mean you have not configured a JTA transaction manager or cache. Not critical but recommended for any serious application. - Mark Felix Dreher <[EMAIL PROTECTED]> 02/16/2006 08:25 PM To: Mark Schreiber/GP/[EMAIL PROTECTED], [email protected] cc: Su

Re: [Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation

ols.enrich(DNATools.createDNASequence("gattacagattaca","urn:local:seq")); As an aside there is no need to cast the return of enrich if you are assining it to a RichSequence pointer. Hope this helps, - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/15/2006 1

Re: [Biojava-l] Genbank parser error [biojavax]

I think these properties should be going to the (Rich)Annotation bundle. - Mark Morgane THOMAS-CHOLLIER <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/15/2006 04:56 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:

Re: [Biojava-l] Genbank parser error [biojavax]

Hi Morgane - Turned out to be a problem with a greedy regexp parsing the LOCUS tag. This is fixed in CVS. Let me know if something else is a problem. - Mark Morgane THOMAS-CHOLLIER <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/14/2006 09:33 PM To: biojava-l@bioja

[Biojava-l] Contributers

t would be really great to keep some kind of record of who contributed what and how many people have contributed to biojava. This will be essential if we ever publish. Don't make me look through the @author tags! - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institu

Re: [Biojava-l] Persist SingleDP object

Hi Martin - You could try the XmlMarkovModel class. It has readModel and writeModel to write markov models as XML. I have used this successfully for models in the past. - Mark Martin Eklund <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/14/2006 12:06 AM To: bio

Re: [Biojava-l] Genbank parser error [biojavax]

the only problem though. Could you post the entire file? Or if it is large then a representative file of smaller size. - Mark Morgane THOMAS-CHOLLIER <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/14/2006 04:36 AM To: [email protected] cc: (bcc: Mark S

[Biojava-l] easy createRichSequence methods

Namespace object. Now available in CVS. - Mark ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] BioJavaX-Hibernate: Namespace problem

ce instead. Then you can specify it's namespace. - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/11/2006 01:55 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] BioJavaX-Hiberna

Re: [Biojava-l] Looking for a RandomAccessFile-like class for sequences

Hello Todd, This sounds a bit like what the biojava BioIndex code does. You make be able to use that. - Mark Todd Riley <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/10/2006 12:02 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/No

[Biojava-l] BioJava wiki

l. As I'm based in Singapore I cannot guarentee the selection process will be entirely transparent : ) Your contributions are welcome. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singap

[Biojava-l] BioJava News site

posted and archived here in future. Thanks, - Mark Mark Schreiber Research Investigator (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

[Biojava-l] biojava wikimedia based home page

ne to copy content over from the current biojava site. We would like to ask for any volunteers who have some experience with Wikimedia who could help out. Please reply to me or to the list. Any help would be greatly appreciated. - Mark Mark Schreiber Research Investigator (Bioinformatics) Nov

Re: [Biojava-l] concatenating chromatograms

()); int[] a2 = c2.getTrace(DNATools.a()); int[] merged = new int[a1.length + a2.lenght] //use a loop here to copy a1 and a2 into merged //now set the DNATools.a() trace for mergeChrom mergeChrom.setTraceValues(DNATools.a(), merged, merged.length); Hope this works! - Mark Heather Kent <[EM

Re: [Biojava-l] Help needed to add "Number of Bits" vertical and column number labeling to DistributionLogos

a visual aid. > >I would like to be able to do this (copied from Samiul Hasan's thesis paper).. take a look at http://www.sanger.ac.uk/Info/theses/ - Mark ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] BioSQL cvs versions

Hello Felix - The best document is the BioJavaX docbook in the docs/ folder of the CVS distribution of biojava. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com

Re: [Biojava-l] Help needed tp add "Number of Bits" vertical and column number labeling to DistributionLogos

several positions in the Logo into one component. The better option is to make the code draw direct to a Graphics2D object. In this way the code can paint to a component or to a BufferedImage. - Mark Todd Riley <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 02/01/2006 05:33 AM

Re: [Biojava-l] Alignment with GAPs

There is no MSA in biojava. CLUSTALW, TCoffee etc are probably much better. "Dickson S. Guedes" <[EMAIL PROTECTED]> 01/28/2006 12:09 AM To: Mark Schreiber/GP/[EMAIL PROTECTED] cc: [email protected], Matthew Pocock <[EMAIL PROTECTED]>

Re: [Biojava-l] Alignment with GAPs

Hi - I think the DP class should accept a GappedSequence. To get the result you want you will probably need to have at least one match state that can emit gaps. I'm curious to know why you would want to do that kind of alignment though? - Mark "Dickson S. Guedes" <[EMAI

Re: [Biojava-l] BioSQL cvs versions

pport the old biojava/biosql mappings after 1.5 is released. They have been deprecated in the CVS. The official way to interact with biosql will be via Hibernate. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #

Re: [Biojava-l] Parse XML BLAST

Which example are you using? The BlastEcho might be faster. - Mark Christian Köberle <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/20/2006 01:16 AM To: bio java mailing list cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] Par

Re: [Biojava-l] getting involved

cool. - Mark "Simon Rouane" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/11/2006 09:36 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] getting involved I'm a commercial Java developer w

Re: [Biojava-l] Generalized HMM in biojava?

Depending on what you mean by generalized You can create lots of custom HMM architechtures using the DP packages of biojava. - Mark wendy wong <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/11/2006 05:00 AM Please respond to sww8 To: [email protected]

RE: [Biojava-l] Embl parser problem[Scanned]

There should only be one copy of the ProjectedFeatureHolder (org.biojava.bio.seq.projection.ProjectedFeatureHolder), Try deleting your biojava-live directory and doing a fresh checkout, make sure you use the -Pd options during the checkout. - Mark "Jolyon Holdstock" <[EMAIL PRO

RE: [Biojava-l] Embl parser problem[Scanned]

directories (new packages since your last update). Or maybe i've got them mixed up, anyhow use both. Try doing a CVS upate -Pd and then running ant. - Mark "Jolyon Holdstock" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/04/2006 06:54 PM To: , <[EMAI

Re: [Biojava-l] Embl parser problem

lease note that if you have access to CVS you could download the development version of the new parsers (biojavax) which do a much better job. - Mark "Jolyon Holdstock" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/03/2006 10:21 PM To: cc: (b

Re: [Biojava-l] Gapping Sequence problems

You could try if(!inGapState && (seq[i].symbolAt(j) == gap || seq[i].symbolAt(j) == AlphabetManager.getGapSymbol())) - Mark "Dan Cardin" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/21/2005 04:16 PM To: [email protected] cc:

Re: [Biojava-l] Locating promoter regions in sequence of DNA with Biojava

anger pages http://www.biojava.org/docs/bj_in_anger/ Other approaches would be programs like MEME or the technique called nested MICA developed by Thomas Down of biojava fame which seems to be very good. - Mark Ilueny Santos <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/16/2005 04

Re: [Biojava-l] Sequence Iteration in BioJava(x)

ryote records). Details on how to do this can be found in the biojavax docboc in CVS. - Mark Mark Fortner <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/16/2005 12:09 PM Please respond to m.fortner To: biojava-list cc: (bcc: Mark Schreiber/GP/Novartis)

Re: [Biojava-l] Sequence Iteration in BioJava(x)

Mark, Thanks for the info. This is sort of a test project for us. We have a few classes and data structures in C++ that handle operations like sequence io and packing, and are fairly fast. However, we've also come to the realization that we've spent a lot of time dealing w

Re: [Biojava-l] Sequence Iteration in BioJava(x)

ght make it hard to say if the java code would be much slower than the C code. - Mark Mark Fortner <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/16/2005 10:36 AM Please respond to m.fortner To: biojava-list cc: (bcc: Mark Schreiber/GP/Novartis) Subj

Re: [Biojava-l] Sequence Iteration in BioJava(x)

ating through the human genome, (and in a number of cases, metagenomic sequences) and we're trying to squeeze as much performance out of it as possible while minimizing the memory footprint. Thanks, Mark Richard HOLLAND wrote: orderNSymbolList splits the sequence into non-overlapp

RE: [Biojava-l] Sequence Iteration in BioJava(x)

the windowedSymbolList woud actually throw an exception cause the sequence above is not evenly divisible by 4 (seq.length() % 4 != 0) - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670

Re: [Biojava-l] somebody can help me?

Hello - If you want to make a Bayesian classifier you would most likely use the org.biojava.dist packages to calculate distributions of nulceotide frequency. Hope this helps, - Mark Ilueny Santos <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/16/2005 04:08 AM

[Biojava-l] Sequence Iteration in BioJava(x)

me to iterate through a sequence this way, or am I on my own? Regards, Mark Fortner ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] SAXException with BLAST errors

Not exactly sure what the problem is here but it looks like your input is not in FASTA format so that might be causing a problem?? "W. Eric Trull" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/13/2005 08:22 AM To: [email protected] cc: (bcc

Re: [Biojava-l] Restriction mapping for the whole chromosome sequence

Have you tried setting the -Xmx option of your JVM? Ilhami Visne <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/12/2005 05:57 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] Restriction mapping for the

Re: [Biojava-l] Hit_def from blast xml output?

You may need to customize your blast listeners. If you run the blast echo example in biojava in anger you will find out what event type that information is contained in. You can then listen for that event type. http://www.biojava.org/docs/bj_in_anger/blastecho.htm - Mark "Michael E.

Re: [Biojava-l] BaumWelchTrainer Broken??!!! (please help)

Fixes for this bug suggested by Todd Riley and Thomas Down are now in CVS. I have tried a few examples and it seems to work well. - Mark ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

RE: [Biojava-l] cvs ant build failure

live distribution but it is good to think about what you may have done to break the unit tests. - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/05/2005 09:42 AM To: "Tamas Horvath" <[EMAIL PROTECTED]> cc: b

Re: [Biojava-l] cvs download

http://www.biojava.org/started.html although it looks like you have done that successfully. - Mark "D.Enrique ESCOBAR ESPINOZA" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 12/01/2005 02:53 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Nova

Re: [Biojava-l] BaumWelchTrainer Broken??!!! (please help)

As a possible work around until this issue can be resolved the BaumWelchSampler can be substituted for a BaumWelchTrainer. Although not technically equivalent they are similar. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10

Re: [Biojava-l] Multiple questions

Regarding the format guessing function. It was deprecated cause it cannot be gaurenteed to work. However, deprecation might be a bit extreme, especially if many people use it. I would propose that we undeprecate it and just document a warning saying it may not work. Any objections? - Mark

Re: [Biojava-l] edit problems with SimpleGappedSequence

Hi - Could you repost some example code of the problem and the version of biojava. Sorry for the tardy responses, everyone seems to be very busy this year. - Mark "Dan Cardin" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/29/2005 07:08 AM To: bioja

Re: [Biojava-l] Multiple questions

Not sure about ClustalW >6) Is there some example-code on how to use DAS (as a client)? take a look at http://www.biojava.org/dazzle/ >7) How can I submit an RFE? No formal proceedure, just post to the list. Even better code it yourself and post it to the list :) - Mark _

Re: [Biojava-l] Using the Meme class

i think the input stream should be reading the output file of Meme. - Mark Te-yuan Chyou <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/24/2005 06:24 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] Usi

Re: [Biojava-l] Annotation

type of Annotation you have? seq.getAnnotation().getClass().getName() This will help us to figure out where the problem is. - Mark "Christian Köberle" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/22/2005 05:58 PM To: [email protected] cc

Re: [Biojava-l] Annotation

OK, that explains it. EMPTY_ANNOTATION is a place holder to avoid getting a null pointer when you ask for the Annotation. It will not let you add properties as it would no longer be EMPTY. Best to not use this unless you don't plan to do anything with the Annotation. - Mark "

Re: [Biojava-l] BaumWelchTrainer Broken??!!! (please help)

Admitidley it's been a very long time since I tried any of these. I'm pretty sure they worked way back then? Matthew, do you have any insights? These are your babies right? - Mark Todd Riley <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/23/2005 05:03 AM

Re: [Biojava-l] BaumWelchTrainer Broken??!!! (please help)

Can you try the code in http://www.biojava.org/docs/bj_in_anger/profileHMM.htm I have found in the past that you need to set some intial weights before starting the BW trainer. If this example doesn't work please repost to the list. - Mark Todd Riley <[EMAIL PROTECTED]> Sent

RE: [Biojava-l] Extract accession number out of xml blast result

/docs/bj_in_anger/blastecho.htm for some hints. - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/11/2005 10:15 AM To: "Andreas Scheucher" <[EMAIL PROTECTED]>, cc: (bcc: Mark Schreiber/GP/Novartis)

Re: [Biojava-l] BioJavaX ready for testing

Richard has done a really excellent job of making some pretty comprehensive docs here with lots of examples. You should be able to use it to take biojavax out for a spin! - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 10/31/2005 05:28

[Biojava-l] substitution matrices and probability

procedure is outlined on page 118 of Durbin et al, Biological Sequence Analysis and in much more detail in Altschul 1991 (J Mol Biol 219: 555-65) - Mark ___ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] Disabling SequencePanel updates

and there may be a better way. - Mark Joel Peter William Pitt <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 10/13/2005 09:46 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] Disabling SequencePanel update

Re: [Biojava-l] Need Help

on on sequence manipulation on this webpage http://www.biojava.org/docs/bj_in_anger/index.htm - Mark "Goh khee Teck" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 10/07/2005 12:30 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Nova

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

ot of development right now so you shouldn't be doing any production programming with them anyway. - 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 297

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

Does SPICE rely on biojava-live? If it only requires biojava1.4 then this wouldn't be an issue. However, if you are actively building SPICE with biojava-live (possibly not a good idea) we can keep it as 1.4 for a while. - Mark Andreas Prlic <[EMAIL PROTECTED]> 10/06/20

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

d 'preview' releases after biojava1.4 will require JDK1.5 (Java 5). If you plan to use new versions of biojava on a machine for which there is or will be no JDK1.5 then you should protest now! - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Disease

[Biojava-l] agave, game, game12

Hello - Does anyone still require or make use of the following packages: org.biojava.bio.seq.io.agave org.biojava.bio.seq.io.game org.biojava.bio.seq.io.game12 They represent i/o classes for these now redundant formats. If not then I will mark them as deprecated and probably remove them when

Re: [Biojava-l] Building from CVS

oders seem to be voting with their feet and a change to 1.5 might be unavoidable. I'm happy with 1.5 but I wonder how many others are stuck with 1.4.2? Which OS's still need a JDK 1.5? Possibly JDK1.5 could begin to be allowed in biojava-live in preparation for biojava1.5?? Anyone pr

[Biojava-l] JDK 1.5

introduced in 1.5 please use the alternative new Integer(i) It even has less typing : ) - 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

Re: [Biojava-l] Graph library

Looks interesting. What is the relationship between cytoscape and GINY? - Mark Gary Bader <[EMAIL PROTECTED]> 10/03/2005 02:23 PM To: Mark Schreiber/GP/[EMAIL PROTECTED] cc: [email protected] Subject:Re: [Biojava-l] Graph library H

[Biojava-l] Graph library

Hello - Does anyone know of a good java graph library that is LGPL, Apache license or similar? Not data graphing but graph as in the mathematical construct. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01

Re: [Biojava-l] Apache License vs. (L)GPL

nable nation : ) My pseudo-legal advice would be to negotiate this directly with the Weka group. Then everyone is happy. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com

Re: [Biojava-l] classpath

ement. - 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 Maxime Caron <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 09

Re: [Biojava-l] Newbie Question: Blast Results Visualization

There is nothing in the biojava packages. However I know that there are people who have written such things in Java/JSP making use of biojava. Anyone want to volunteer some code? - Mark Renee Halbrook <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 09/20/2005 06:54 PM

RE: [Biojava-l] 3 questions and problems

ikely anyone would want to store a sequence with * in it so all biojava protein sequences could be stored and read as protein. Having said that I'm sure someone somewhere will try it : ) - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 09/20/2

Re: [Biojava-l] 3 questions and problems

integer. The value of the constant is probably irrelevant (it's a constant) so you could convert back again as long as you can normalize to 1.0. This is not perfect as you get some rounding errors but it should be close enough. By the way, it seems your alignment classes have not been

Re: [Biojava-l] Global Sequence Alignment

get you a smith-waterman as well? - 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 "Andreas Dräger" <[EMAIL

[Biojava-l] [offtopic] biojava developers in the UK

pt to the 15th of Sept. Please post replies directly to my gmail address (markjschreiber {at} gmail.com). I will not frequently monitor my work mail or this list so this will be the best way to contact me. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tro

Re: [Biojava-l] SCF parser problem

Hello - I may have missed that patch. Can you send me the source for the corrected SCF parser and I will commit it to CVS so it makes the next version. Thanks, - Mark Andy Yates <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/25/2005 10:55 PM To: "Zhao, Yongm

Re: [Biojava-l] sequence masking?

softmasked version of 'DNA' FiniteAlphabet alpha = SoftMaskedAlphabet.getInstance(DNATools.getDNA()); //Make a symbol list over that alphabet SimpleSymbolList syms = new SimpleSymbolList(alpha.getTokenization(), "ACCTCGCTTCGA"); //do stuff ... - Mark

Re: [Biojava-l] parse (recent) blast output

r you should be able to find out what is going wrong. - 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 Dominique Vlieghe &l

RE: [Biojava-l] Newbie Installation Question

don't require these to be unzipped either. If you are not using an IDE you will need to unzip them so you can view them. - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/22/2005 09:38 AM To: <[EMAIL PROTECTED]>, <[EMAIL PR

Re: [Biojava-l] ZTR trace file parser?

AFAIK there is only SCF and ABI formats. If someone wants to add ZTR that would be great. - Mark "Zhao, Yongmei" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/19/2005 03:37 AM To: cc: (bcc: Mark Schreiber/GP/Novartis) Subject:

Re: [Biojava-l] RNA alignment

Hello - This example explains how you can do a pairwise alignment with a hidden markov model. There is no specific implementation of a local alignment (eg smith waterman). I've been thinking about it but I haven't gotten around to it. - Mark "Christian Köberle" <

Re: [Biojava-l] Construct a phylogenetic tree

Hello - If your on windows you can use a program called TreeView. There is also a Java package called PAL that can draw and manipulate trees and do lots of phylogenitic calculations. Not sure of the web site. Try google. -= Mark Jan Würthner <[EMAIL PROTECTED]> Sent by: [EMAIL PRO

[Biojava-l] Gibbs sampling demo

Hello - I have put an example of how you can build a gibbs sampler using biojava on the web at http://www.biojava.org/docs/bj_in_anger/gibbs.html It's pretty simple to do and makes a lot of funky use of the Distribution class. Enjoy! Mark Schreiber Principal Scientist (Bioinform

Re: [Biojava-l] Reverse transcription

>I just wanna note that if somebody writes it up for the cookbook, note >that the code snippet by Mark isn't symmetric with transcribeToRNA(). >I put in a DNATools.complement() to make it just so. Changing strand, alphabet and polarity all in one go

Re: [Biojava-l] Reverse transcription

hod does the opposite. Anyone want to wirte that up for Biojava in Anger? - Mark Jacob Rohde <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/15/2005 04:26 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:Re: [Biojava-l

Re: [Biojava-l] Reverse transcription

See also DNATools.transcribeToRNA(), especially read the javadocs and contrast that with DNATools.toRNA(). Jacob Rohde <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/13/2005 09:17 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) S

Re: [Biojava-l] Reverse transcription

Take a look at http://www.biojava.org/docs/bj_in_anger/ReverseComplement.htm Jacob Rohde <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/13/2005 09:17 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject:[Biojava-l] R

Re: [Biojava-l] Compress Sequences.

ou could use this as the bases for full LZ compression. There are also very much more complicated algorithms published that look for long range repeats, these are also very slow. - Mark Felipe Albrecht <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/12/2005 04:07 AM To:

[Biojava-l] biojava and matlab

Hello all - I stumbled across this today, it might be of interest to people who use matlab and want to call biojava functions from it. http://www.mathworks.com/company/newsletters/digest/2005/july/integrate_matlab.html - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis

RE: [Biojava-l] Sequence and String

STDOUT or similar. It shouldn't be used in algorithms or general programing. - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 08/06/2005 12:49 PM To: "Felipe Albrecht" <[EMAIL PROTECTED]>, cc:

Re: [Biojava-l] Cast to Sequence

You might also want to use the Biojava FeatureTree class. An example of it's use is at http://www.biojava.org/docs/bj_in_anger/treeView.htm - Mark Jacob Rohde <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 07/31/2005 08:36 PM Please respond to Jacob Rohde To:

Re: [Biojava-l] Protein CharacterTokenization

Hello - Can you provide some example code? Any protein ambiguity should map to X. Unlike DNA which has lots of ambiguity codes with different meanings. BioJava can support all kinds of protein ambiguity but when they are tokenized they should all end up as X. - Mark "Tal Blum&quo

Re: [Biojava-l] (no subject)

s/opinions from people using bio-java. >or anyother bio-java related information would be helpful. >Any assistance would be much appreciated. > >Cheers, >Daniel Park You might want to put a survey form somewhere on the web. We have never done a survey of biojava users and the resul

Re: [Biojava-l] Trouble with GOParser

Hi - Can you post the entire stack trace and the version of biojava you are using to the list (not direct to me as I'm not an expert on this API)? - Mark "Óscar D. Sánchez Jiménez" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 07/14/2005 10:37 PM To:

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