EMBOSS 6.3.1 at CSC

26.07.2010

The EMBOSS sequence analysis package has been updated to version 6.3.1. The new version available in Hippu, Murska and Vuori servers and in Scientist's Interface.

The new EMBOSS version is capable of retrieving sequence data directly from the Ensembl mysql-server in EBI.  A slightly modified USA definition is used  the case of Ensembl sequences. The format is ensembl:species:ID-code

For example:

seqret ensembl:mouse:ENSMUST00000103109
infoseq ensembl:human:ENST00000262160
showseq ensembl:homo_sapiens:ENST00000262160

EMBOSS can now read sequence data also from other MySQL or ProtgeSQL databases.

Another enhancement is the improved capability of manage next generation sequencing data formats. In addition to fastq and sam EMBOSS can now read and write also bam formatted files. For example converting sam formatted file into bam format can be done with command:

seqret ngs_alignment.sam bam::ngs_alignment.bam

More information about the new EMBOSS version  and its usage at CSC can be found from:

http://www.csc.fi/english/research/sciences/bioscience/programs/emboss/