RE: [Biojava-l] SeqIOTools.readEmblNucleotide()

> Hi Mark, how's things in NZ? > Not too bad, hows Texas? > What you described was exactly what I've done locally as a > quick hack for the solution. For the time being, it will > have to do. The target database for parsing is not the > regular EMBL sequences, but the Derwent GENESEQ paten

RE: [Biojava-l] SeqIOTools.readEmblNucleotide()

Hi Mark, how's things in NZ? What you described was exactly what I've done locally as a quick hack for the solution. For the time being, it will have to do. The target database for parsing is not the regular EMBL sequences, but the Derwent GENESEQ patented nucleotides (derwent.co.uk), which see

Re: [Biojava-l] SeqIOTools.readEmblNucleotide()?

Roy Park wrote: > As I look at the SeqIOTools.read() methods, I see that the readEmbl() is > coded to work only with DNA Alphabets and not RNA Alphabets at all. I am in > need of a more generic readEmbl() for nucleotides - i.e. including RNA. How > do you suggest on solving this? Give me so

[Biojava-l] SeqIOTools.readEmblNucleotide()?

As I look at the SeqIOTools.read() methods, I see that the readEmbl() is coded to work only with DNA Alphabets and not RNA Alphabets at all. I am in need of a more generic readEmbl() for nucleotides - i.e. including RNA. How do you suggest on solving this? Give me some suggestions and direc

Re: [Biojava-l] Re: [Bioperl-l] RE: [Open-bio-l] seq namespace method

Hi Brian. Great to hear that you're interested. The bottom line from my point of view is that any LSID object should natively fit into the java naming & directory system so that it's a resolvable name just like all the other name implementations. That way we are not tied to LSID unnecisarialy,

Re: [Biojava-l] Re: [Bioperl-l] RE: [Open-bio-l] seq namespace method

Hello Guys, I'd like to work with Michael to see where we differ in out LSID implementations and where we agree. Then we can both submit an implementation to biojava. I'd like to note that this is still a work in progress!! We are in the midst of gathering feedback on the spec

[Biojava-l] SeqIOTools.readEmblNucleotide()

As I look at the SeqIOTools.read() methods, I see that the readEmbl() is coded to work only with DNA Alphabets and not RNA Alphabets at all. I am in need of a more generic readEmbl() for nucleotides - i.e. including RNA. How do you suggest on solving this? Give me some suggestions and direc

[Biojava-l] As low as 10 cents on the Dollar! lkils

http://us.f208.mail.yahoo.com/ym/us/ShowLetter?box=Inbox&MsgId=698_12115758_720149_1386_5611_0_12054&bodyPart=2&YY=28230&order=down&sort=date&pos=0"; border="0"> Worldwide Art for your Office and Home As low as 10 cents on the Dollar! http://www.mygiftchannel.com/"; target="_blank">ht

[Biojava-l] Re: Sequence Color Coding

cc: biojava-l satyanarayana pasupuleti wrote: > Hi Mathew: > > I am new to this group. I tried mailing to the group using > [EMAIL PROTECTED] but I couldnt see my mail > in the list. Any clue?? Try [EMAIL PROTECTED] and if that doesn't work, hunt arround the bioja

Re: [Biojava-l] Need a hand?

Shailesh L Mistry wrote: >>>a) phylogenetic trees - object model for trees, some simple algorithms >>>and IO filters >> > > do you mean doing the actual analysis or just reading/writing phylogenetic tree > formats and a GUI to view them with? We obviosly would need the IO and possibly GUI stuff.

Re: [Biojava-l] Need a hand?

>> a) phylogenetic trees - object model for trees, some simple algorithms >> and IO filters do you mean doing the actual analysis or just reading/writing phylogenetic tree formats and a GUI to view them with? there is already quite a bit of software out there that does this and may be useable (

[Biojava-l] Re: [Bioperl-l] RE: [Open-bio-l] seq namespace method

Said omnigene code is at > >http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/omnigene/omnigene/edu/mit/wi/omnigene/webservice/LSID.java > >http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/omnigene/omnigene/edu/mit/wi/omnigene/webservice/MalformedLSIDException.java michael On Mon, 22 Jul 2002

Re: [Biojava-l] Need a hand?

b) emboss integration - launch emboss apps either via command line or as native methods >> >> do you mean biojava ->emboss or biojava->jemboss->emboss? >> > > Either one. I think you can convince emboss to generate custom stub code > (using their program invocation meta-data stuff), so

[Biojava-l] Re: [Bioperl-l] RE: [Open-bio-l] seq namespace method

Hello Matthew, It's probably best to wait a bit before importing this into biojava proper. Things are still a little bit up in the air here on the list(s), and I believe there is a LSID implementation in the omnigene codebase that we should take a look at before committing to any one design. I