Trimmomatic: flexible trimmer for Illumina sequence data

Developer's note

Developed defined Trimmomatic as a tool that 'performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.'


Anthony M. Bolger, Marc Lohse, and Bjoern Usadel
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bioinformatics 2014 doi:10.1093/bioinformatics/btu170


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comTAR :conserved Plant microRNA targets prediction and characterization tool

Developer's note

Developed defined comTAR as a tool that 'allows users to analyze the variations of known miRNA targets during evolution and to predict previously unknown interactions by focusing on the conservation of the potential targeting.'


Uciel Chorostecki and Javier F. Palatnik
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants.
Bioinformatics doi:10.1093/bioinformatics/btu147


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BioJava 3.0.8 : New Version of BioJava released

So if you are a Java Bioiformatician fan then it is a good news for you.Developers of BioJava has recently announced the release of BioJava 3.0.8. New version of BioJava,BioJava 3.0.8, includes several new features as well as a lots of bug fixes and improvements. Just like BioPerl, you can also download BioJava modules from their download page.


Script name Download
BioJava 3.0.8
5 'Bio' Programming Language You May Use HERE

New Features

- new Genbank writer
- new parser for Karyotype file from UCSC
- new parser for Gene locations from UCSC 
- new parser for Gene names file from
- new module for Cox regression code for survival analysis
- new calculation of accessible surface area (ASA)
- new module for parsing .OBO files (ontologies)
- improved representation of SCOP and Berkeley-SCOP classifications

Learn PERL Basic with Me : NCBI BLAST parser IV

Learn PERL Basic with Me : NCBI BLAST parser III