JAE: Jemboss Alignment Editor.

Unlabelled: One of the most basic methods of understanding the biological significance of a sequence is to produce an alignment with related sequences. A vital aspect of correctly aligning sequences is to apply biological intuition through manual editing of an alignment produced by multiple-sequence alignment software. As part of the European Molecular Biology Open Source Software Suite (EMBOSS), a new alignment editor in the Jemboss package is freely available for download.

Molecular characterisation of the SAND protein family: a study based on comparative genomics, structural bioinformatics and phylogeny.

The activities of vertebrate lysosomes are critical to many essential cellular processes. The yeast vacuole is analogous to the mammalian lysosome and is used as a tool to gain insights into vesicle mediated vacuolar/lysosome transport. The protein SAND, which does not contain a SAND domain (PFAM accession number PF01342), has recently been shown to function at the tethering/docking stage of vacuole fusion as a critical component of the vacuole SNARE complex.

Jemboss reloaded.

Bioinformatics tools are freely available from websites all over the world. Often they are presented as web services, although there are many tools for download and use on a local machine. This tutorial section looks at Jemboss, a Java-based graphical user interface (GUI) for the EMBOSS bioinformatics suite, which combines the advantages of both web service and downloaded software.

Tutorial section: domains and motifs - proteins in bite-sized chunks.

Possibly the ultimate goal of bioinformatics is to be able to predict protein tertiary structure and chemical functionality from the initial amino acid sequence. Despite the best efforts of many researchers over the past two decades, a reliable modelling method has yet to be found and the folding problem continues to be a hurdle for scientists.