I have a small problem... I know that for download a PDB structure using BioJava I should use What I should do to use mmCIF file instead? ...

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 ...

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): ...

I've created an image of a chromatogram (of a dna sequence). How would I go about putting a number over each basecall? I can get the pixel length of ...

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.bio ...

I've tried to run a very simple sample BioJava copy&pase from wikipedia. However, when I run it I get the following exception: Version: ...

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 ge ...

I am trying to do a structural alignment using BioJava libraries. I want to pick some chains from one structure object one by one and add them to anot ...

Is there any method to use in biojava to predict secondary structure from a given sequence? Or if not does any anyone how can i implement it? any sou ...

I would like to ask if there is possible using biojava add sequence to exiting profile alignement ? I mean I would like to keep my existing profile st ...

I have problem with multiple sequence alignement. I have two sequences as follow and I m trying to align them using biojava methods and I get error li ...

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 util ...

I am having problems with running my code by using Eclipse on Windows 8. The code below runs smoothly in Eclipse on Linux but not in Windows 8. Bas ...

I have downloaded biojava jar files and kept in my classpath. I am trying example to test from : http://www.biojava.org/wiki/BioJava:CookBook:Core:Fas ...

I am new to programming and would like to use a class from Biojava3. Specifically the getDNACodingSequences method from GeneIDXMLReader class. When ...

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 whe ...

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 ...

Here is a typical input .txt file (also called as fasta file): Code to read the sequence may be found here. It gives the proper output, as shown b ...

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 ac ...