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Eman Alhaweri | 17 Jun 2013 20:24
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Problem in Digestion with Symbol 'X'

Hi

I am working with Biojava in my Master project but I have problem and I
hope if you can solve it for me. The protein database that I use in my
project is contained Xs which is unknown symbol. When I tried to digest the
protein sequences, Biojava gave an error that X is unknown symbol. Please
tell how can the sequence pass the digestion without error.

The error is: Exception in thread "main"
org.biojava.bio.symbol.IllegalSymbolException: The mass of the symbol [VAL
ILE GLY ALA CYS MET SEC GLU HIS THR PYL TYR SER TRP GLN PRO ASP LEU ARG LYS
ASN PHE] is unknown

 Thanks in advance.
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Phelelani Mpangase | 13 Jun 2013 10:11
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Working with mmCIF files

Hello

I am new to the Java progrmming language, and I am currently working on a
project where I have to find information about a protein structure from the
mmCIF file. I would like to extract information about non-polymers in
structures (_pdbx_entity_nonpoly table) using BioJava. How do I go about
achieving this?

I have been able to parse the structure using the SimpleMMcifConsumer, but
I am unclear as to the steps I need to follow from there. Is the
PdbxEntityNonPoly the right class to use? How do I use this class to
achieve to get the data from the "_pdbx_entity_nonpoly"?

Regards,
Phele
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Khalil El Mazouari | 11 Jun 2013 18:10
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Re: Biojava-l Digest, Vol 125, Issue 2

Hi Andreas,

thanks for the feedback.

increasing gop and gep was not sufficient. I had to use a modified version of nuc-4_2 scoring matrix where I
set the mismatch value very low. This solved the problem,

Best

khalil

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On 11 Jun 2013, at 18:00, biojava-l-request <at> lists.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
> 	biojava-l <at> lists.open-bio.org
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Khalil El Mazouari | 9 Jun 2013 21:32
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Local aln - contig assembly

Hi,

I am trying to assemble overlapping sequence (direct & reverse) via local alignment. I am only searching
for local aln with 100% identity.

Which parameters, matrix ... should I use in order to get 100% ident. local aln.

Any other suggestion for assembling overlapping seq (in Java) is welcome.

Thanks

khalil

   SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_2();
   SimpleGapPenalty gapP = new SimpleGapPenalty();
   gapP.setOpenPenalty((short) 5);
   gapP.setExtensionPenalty((short) 1);
   SequencePair<DNASequence, NucleotideCompound> psa =
   Alignments.getPairwiseAlignment(query, target,
   PairwiseSequenceAlignerType.LOCAL, gapP, matrix);

========

Local Alignment Identity: 97.84688995215312%

query     GGGGAAAACACGAAAGGCCCTTGGTGGAGGCGCTTGAGACGGTGACAAGGGTTCCCTGGC  68
          |||||| || |||  ||||||||||||||||||||||||||||||| |||||||||||||
target    GGGGAAGAC-CGATGGGCCCTTGGTGGAGGCGCTTGAGACGGTGACCAGGGTTCCCTGGC 417

query     CCCAGTAGTCAAAGGTCCGTGAGGAGCTCCACTTGTGTGCACAGTAATATGTGGCTGAGT 128
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Christina Nilofer | 29 May 2013 13:52
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Regarding the transcription script

Hi Sir,

This is christina,

In your code for transcription input was "atgccgaatcgtaa"
and the output was   "augccgaaucguaa".
 Here in this you have replaced t's with u's but the output must be
"uacggcuuagcauu"

we are not changing dna to rna, we are transcribing.

--

-- 
*Christy*
**
**
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Ben Bimber | 23 May 2013 20:53
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reading genbank data

Hello,

To date, I have used BioJava3 for very limited work such as read/writing
FASTA files.  I am trying to determine the best method to read and parse
sequence in genbank format using java.  As far as i can tell, legacy
BioJava has classes to support this (RichSequence.IOTools); however, I do
not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
have support for parsing genbank files?

Thanks in advance for any help.

-Ben
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Janier J. Ramírez | 16 May 2013 15:51
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help with fastq

Hi again comunity !

I need this time generate a Fastq file from many fasta files, using illumina scores (one default value).
I ´ve tried this but am having a problem wthis the header and the identifier of the file.
makes Biojava this work ?

greetings

Janier
--

-- 

Universidad de las Ciencias Informáticas 
Janier J. Ramírez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu

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Janier J. Ramírez | 13 May 2013 16:21
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File formats parser

There is in Biojava a parser for some of the next file formats ?? :
.sam
.bam
.gig
.ace 

thanks in advance
--

-- 

Universidad de las Ciencias Informáticas 
Janier J. Ramírez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu

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Hannes Brandstätter-Müller | 8 May 2013 06:21

Re: Getting reverse complement

I missed posting my answer to the list too.

Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ramírez :

> Yes, already it works fine, thanks !
>
> Janier
>
> ----- Mensaje original -----
> De: "Hannes Brandstätter-Müller" <biojava <at> hannes.oib.com <javascript:;>>
> Para: "Janier J. Ramírez" <jjramirez <at> estudiantes.uci.cu <javascript:;>>
> Enviados: Miércoles, 8 de Mayo 2013 5:59:54
> Asunto: [Biojava-l] Getting reverse complement
>
> Usually, gaps are signified by - (probably . works too)
>
>
>
>
> Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ramírez :
>
>
> I'm triyng to get the reverse complement from a sequence with gaps
> (represented as ':'), but biojava thow an IllegalSymbolException, is this a
> bug or what is the symbol to represent gaps in biojava ?
>
> Here is the error.
>
>
> org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
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Janier J. Ramírez | 8 May 2013 05:51
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Getting reverse complement

I'm triyng to get the reverse complement from a sequence with gaps (represented as ':'), but biojava thow an
IllegalSymbolException, is this a bug or what is the symbol to represent gaps in biojava ?

Here is the error.

org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: ':'
	at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
	at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
	at org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
	at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)

Greetings

Janier

--

-- 

Universidad de las Ciencias Informáticas 
Janier J. Ramírez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu

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Spencer Bliven | 7 May 2013 22:27
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Re: AMOScmp problem

Janier,

Biojava 1 is only receiving bug fixes currently. There are a couple changes
since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
maven repository. There is no release date for 3.0.6 yet, but again you can
use the latest SNAPSHOT from maven if you need new features.

-Spencer

On Tue, May 7, 2013 at 12:31 PM, Janier J. Ramírez <
jjramirez <at> estudiantes.uci.cu> wrote:

> When Biojaba 1.8.3 will be released ?
>
> cheers
>
>
> ----- Mensaje original -----
> De: "Spencer Bliven" <sbliven <at> ucsd.edu>
> Para: "Janier J. Ramírez" <jjramirez <at> estudiantes.uci.cu>
> CC: "Biojava-l <at> lists.open-bio.org" <biojava-l <at> lists.open-bio.org>
> Enviados: Martes, 7 de Mayo 2013 21:00:44
> Asunto: Re: [Biojava-l] AMOScmp problem
>
>
>
>
> Hey Janier,
>
> Sorry no one responded to your last question. Biojava doesn't currently do
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Gmane