biojava
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biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
would be great to be able to create a Profile from some of the popular file formats for representing multiple sequence alignment files. Currently we can read Stockholm files like...
see discussion on the mailing list http://mailman.open-bio.org/pipermail/biojava-l/2015-March/011367.html
I encountered an Exception when trying to parse some structures, with something that seems related to insertion codes. The two I looked at are obsoleted, so it may be a...
D2 cases use a cube for the polyhedron representation. The main (red) axis goes through a face, but the other axes are oriented to go through edges. For instance, [5AVP](http://www.rcsb.org/pdb/explore/jmol.do?structureId=5AVP&opt=3&bionumber=1):...
The alignments are defined in such a way that it is not possible to have consecutive gaps. Here's a test case (to go in NeedlemanWunschTest. Requires 4bc1d20.): ``` java @Test...
The structural alignment algorithms currently implemented in biojava, **CE** and **FatCat**, have a common characteristic: they are **sequential**. This means that they assume that the topology of the structures compared...
SCOP2 was recently published: [[server]](http://scop2.mrc-lmb.cam.ac.uk/) [[paper]](http://nar.oxfordjournals.org/content/early/2013/11/29/nar.gkt1242.full) BioJava should eventually include a parser for the data. This could be similar to the ScopDatabase interface & implementations, but would need an updated...
Add a parser for [MrBayes](http://mrbayes.sourceforge.net/) output. _Suggested for [GSoC 2012](http://biojava.org/wiki/Google_Summer_of_Code_2012)_
Variation APIs that bring together Ensembl Variation, VCF file format, GFF3+GVF file format, samtools, Picard, GATK, etc. Several similar file specifications exist for dealing with sequence variation, including: - VCF...
I'm trying to implement an amino acid frequency calculator. I've finished it but I'm using `Sequence.countCompounds` and it is _incredibly_ slow. I'm profiling this with the `JVM Monitor` plugin for...
