What is new in Sockeye 1.1

• Comparative genomics

• Tools for sequence alignments have been enhanced.
• A Smith-Waterman method has been added.
  
• For any alignment, pairwise or multiple, you can dynamically configure sequence conservation profiles and can show conserved regions in genomic context on aligned or  original tracks.
• A basepair-level alignment viewer shows sequences, sequence conservation profiles and conserved regions.
  
• You can export two types of alignment data: the gapped sequences in either MultiFASTA or CLUSTAL format, and sequence conservation profile scores.
  

• Regulatory elements

• Text file 'libraries' of transcription factor binding site (TFBS) matrices can be browsed in a catalog. Groups of matrices drawn from the catalog can be saved and reused.
  
• The default TFBS library is the JASPAR collection.
  
• You can easily extend the TFBS libraries by creating text files in either TRANSFAC or JASPAR format.
  
• For word and matrix discovery, the ELPH Gibbs sampler and the Teiresias pattern discovery algorithm are now available.
  
• Single or multiple sequence regions can be scanned with PWMs, or analyzed with the pattern discovery methods. Pattern and PWM hits are displayed as scored features in genomic context.
  

• Importing Data

• EnsEMBL database queries and GFF file imports have been combined in a simple data retrieval wizard.
  
• You can now retrieve a genomic region by entering a gene's EnsEMBL ID.
  

• Dynamic data range

• 'Semantic zooming' (SZ) displays features as histograms for track data windows that are too large to make a display of individual features meaningfull.  SZ lets you freely work on any genomic scale between the karyotype and the basepair, and delivers results for long regions quickly.

• Stability

• Many bugs have been eliminated.
  

• Java
  

• Sockeye for Linux uses Java 1.4.1 and Java3D 1.3.1 beta 1.

• Sockeye for Windows uses Java 1.4.2 and Java3D 1.3.1.