What has changed in SAMS versions?

New features such as a TC update feature, or new tools for functional analysis such as HAMAP, PRIAM and an extended search interface, PatScan search for sequence patterns were added in the new SAMS release. Additionally, a web service based integration of microarray expression data has been implemented as well as the vizualisation of the corresponding experimental results.

In addition to a lot of small improvements there are some new features implemented:

• Project states (avoiding conflictig actions)
• Configurable Metanor (=automatic annotation pipeline)
• Job and Annotation statistics
• Pie-chart views of functional classification distributions
• SteN - Statistical electronic Northern blot

This new version includes numerous bug-fixes over SAMS 1.4 and presents some features which have been implemented in order to meet the users needs and suggestions. Here is a list with the main topics that have been worked out in SAMS 1.6:

• Coloured visualization of the sequence data sets, according to the quality of database matches.
• Option to filter the sequence data according to their E-value. (The filter facility has been completely re-written.)
• Option to export the chosen sequence data into (multiple) FASTA files, tab-separated files of into EMBL format.
• Option to join two or more existing libraries allowing the clustering and assembly of different sequence sets.
• Option to setup user defined BLAST Tools.
• Improved BLAST interface included.

It includes numerous bug-fixes over SAMS 1.2 and presents some features which have been implemented such as:

• Improved importer - some backend changes led to a much faster import of sequences, avoiding "time-outs".
• Manifold filter options in the sequence data viewer, compared to SAMS 1.2.
• Improved job status information of imported sequences.
• Only TCs and singlets can be annotated. The ESTs get the annotation of the corresponding TCs during export or publication.

The release 1.2 of SAMS supports the analysis of shotgun reads within whole genome sequencing projects, as well as EST sequences, covering prokaryotic and eukaryotic data analysis.