BioJava is an open-source project dedicated to providing a Java framework for processing biological data.
BioJava is an open-source project dedicated to providing a Java framework for processing biological data.
Questions tagged [biojava]
28 questions
3
votes
1 answer
Bioinformatics - Need to get the ATOMS sequence
I search a method in BioJava to get the Atom sequence from a PDB file.
I watched the BioJava API but for the getAtomSequence() it catches the amino acids.
I tried with several other method in BioJava but nothing worked as I want.
Can anybody help me…
Yo_O
- 31
- 1
3
votes
2 answers
Java Bioinformatics - get all indexes of multiple specific words in a string
I have a project in my Bioinformatics course at the university, and one of the things in my project is gene prediction.
My problem today is how to get all indexes of more than one specific word in a string. For example, in my case here I want to…
Wrix789
- 35
- 6
2
votes
6 answers
What is a good way to implement getting a consensus sequence in Java?
I have the following problem:
I have 2 Strings of DNA Sequences (consisting of ACGT), which differ in one or two
spots.
Finding the differences is trivial, so let's just ignore that
for each difference, I want to get the consensus symbol (e.g. M…
brandstaetter
- 932
- 3
- 13
- 30
2
votes
1 answer
Calculating physico-chemical properties of amino acids in Biojava
I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava.
I have found in the BioJava tutorial how to read the Fasta files and…
arteagavskiy
- 57
- 5
1
vote
0 answers
How to get differences between amino acid sequences in java?
I would like to get differences between 2 amino acid sequences after alignment
For example from:
target: LTTYEYLDDCRDDEE
query: LATYYYLDDCRDDEE
I would like to know amino acid changes and where it occurs.
Here is my code:
//alignment
try…
vmicrobio
- 331
- 1
- 2
- 13
1
vote
0 answers
Building BioJava 5.0 with Maven on Windows 10
On a Windows 10 machine with Maven 3.5.3 and Eclipse (Oxygen) installed, I attempted to build Biojava. Unfortunately, the following output appeared after I followed the steps listed in the site, http://download.eclipse.org/egit/updates/, and I don't…
CaitlinG
- 1,955
- 3
- 25
- 35
1
vote
0 answers
Biojava: Package import errors
The following code:
import org.biojava.bio.structure.ResidueNumber;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.io.PDBFileReader;
import org.biojava3.protmod.structure.ProteinModificationIdentifier;
public class…
CaitlinG
- 1,955
- 3
- 25
- 35
1
vote
1 answer
How can I use mmCIF format instead PDB in BioJava?
I have a small problem...
I know that for download a PDB structure using BioJava I should use
Structure s = StructureIO.getStructure("code");
What I should do to use mmCIF file instead?
fafnir1990
- 185
- 2
- 16
1
vote
1 answer
Biojava : HET aminoacids
Reading pdb structure 2a65 I am facing the case of an aminoacid residue that should be considered a "ligand of the protein" rather than a "part of the protein".
In the PDB file as well as cif files, this LEU.601 residue is tagged as HET,…
Benjamin Schwarz
- 21
- 6
1
vote
2 answers
Can't get biojava to work in a Maven Netbeans application
I have a problem getting BioJava to work in a Netbeans RCP application, built using Maven. I've created a Maven module as a wrapper, including org.biojava.* and org.forester.* packages as public in the POM. Then, from another module I set the…
Henk van den Toorn
- 11
- 4
1
vote
0 answers
atomchace function in biojava
Hi everyone I'm fairly new to biojava and trying to implement this piece of code:
AtomCache cache = new AtomCache();
cache.setPath("/tmp/");
FileParsingParameters params =…
Mossig Stamboulian
- 17
- 5
1
vote
2 answers
Retrieving whole genome genbank files for some organism using Biojava or Biopython
does anyone have an idea how to automatically search and parse gbk files from FTP ncbi using either BIopython or BioJAVA. I have searched for the utilities in BIojava and have not found any. I have also tried BioPython and here is my Code:
from Bio…
user3419642
- 27
- 1
- 6
1
vote
1 answer
Conversion of GenBank format file to FASTA format
I am quite new to Java and want to build a program that can convert a GenBank text file to FASTA format. Basically there will be two texboxes: one where I will upload the GenBank format file, and a second to show the converted FASTA format…
Sonal Akhal
- 15
- 9
0
votes
2 answers
Steps to read the text file into specific columns of JTable using biojava
Here is a typical input .txt file (also called as fasta file):
>contig00001 length=586 …
mif
- 1
0
votes
1 answer
How to integrate confidence values into DNA chromatogram images?
I'm using biojava to create a chromatogram.
The chromatogram is an image. Each basecall is held within a rectange.
To get x coordinate (left side): gfx.getCallboxBounds(int i).getX();
To get width: gfx.getCallboxBounds(int i).getX()
where the…
Kicking Bird
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