?
Anyone who can help me out here?
Thank you and regards,
Stein Aerts, Katholic University Leuven, Belgium.
--
java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException
at org.biojava.bio.seq.SubSequence.(SubSequence.java:62)
at
Hello,
does anyone know how to get an ensembl gene id out of the Ensembl database
(kaka.sanger.ac.uk) starting from a list of locuslink id?
Thanks a lot,
Stein Aerts
ESAT-SCD, KULeuven, Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI/
winmail.dat
Description: application/ms-tnef
features on a subsequence (ChangeVetoException). Can a
subsequence not be casted to a sequence?
Thank you and kindest regards,
Stein Aerts.
ESAT-SCD, Katholic University Leuven, Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI/
winmail.dat
Description: application/ms-tnef
Hello,
does anyone have experience matching matrices from the Transfac library of
transcription factor binding sites to a sequence? In other words, would
there be a biojava method that covers the functionality of programs like
Matinspector or Match?
Thanks in advance,
Stein Aerts.
Ir Stein
)
ENSG0114251: exon|-|[117,201]|
ENSG0114251: source|[1,2201]|
ENSG0114251: CDS|[117,201]|
Now the last CDS is not stranded anymore. Could the reason be that this CDS
has a joined location in the original sequence? Because the exon still has
its strand.
Thanks & bye,
Stein Aerts.
Hi,
Could somebody point me to some example code that parses an EMBL entry in
AGAVE (or BSML) format into a biojava sequence object? For use with XEMBL.
Thanks a lot,
Stein Aerts.
Ir Stein Aerts
Bioinformatics Research
KULeuven, ESAT-SCD
Kasteelpark Arenberg 10
3001 Heverlee, Belgium
Tel +32
w and example sequence files in attachment.
Best regards,
Stein Aerts.
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.*;
import java.io.*;
public class TestEmbl {
public static void main(String[] args) throws Exception {
Sequence seq =
first
case I need a StrandedFeature, in the second a Feature, but that puzzles me.
Any ideas or examples?
Thank you!
Stein Aerts.
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Exception in thread "main" java.lang.NoSuchMethodError:
sista.sequence.HumanGene.makeMySubSeq(IILjava/lang/String;)Lorg/biojava/bio/
seq/impl/SimpleSequence;
at Syntenous.getSeq(Syntenous.java:66)
at Syntenous.main(Syntenous.java:23)
Does anyone have an idea where such an error m
be anyone who could help me out on this?
Thanks a lot,
Stein Aerts.
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nger.ac.uk database?
Thank you!
Stein Aerts.
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Would there be a reason why there is no "score" and "frame" field in the
Feature.template class? If they are not present in a Feature, then how
can they be outputted using a GFFWriter?
Stein.
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http://bi
useful, I could
consider cleaning up my code for this purpose.
Thank you BioJava!
Best regards & all comments are appreciated,
Stein Aerts.
--
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI
___
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/end_phase=0
Thank you in advance!
Stein.
--
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI
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I'm not at all dependent on EMBL files. I only need a sequence with some
annotation and some features. Any format that is parsable with BioJava
would do. What alternatives are currently at hand?
Stein.
Arne Stabenau wrote:
Stein Aerts wrote:
OK, then we will wait until monday.
14) 343-6111 x.4066
Courriel: [EMAIL PROTECTED]
===
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--
Stein Aerts [EMAIL PROTECTED]
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI
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