Assuntos
Biologia Computacional/métodos , Alinhamento de Sequência , Análise de Sequência de DNA , Análise de Sequência de Proteína , Alinhamento de Sequência/estatística & dados numéricos , Análise de Sequência de DNA/estatística & dados numéricos , Análise de Sequência de Proteína/estatística & dados numéricos , SoftwareRESUMO
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. The Jemboss Alignment Editor (JAE) incorporates standard methods of editing, and colouring residues and nucleotides to highlight important regions of interest. JAE also makes use of scoring matrices (PAM and BLOSUM), selected by the user, to display regions of high degrees of similarity and identity. Other tools include the ability to calculate a consensus, a consensus plot (using a selected scoring matrix) and pairwise identities. AVAILABILITY: The JAE can be launched from the webpage (http://emboss.sourceforge.net/Jemboss/).
Assuntos
Algoritmos , Proteínas/química , Alinhamento de Sequência/métodos , Análise de Sequência de Proteína/métodos , Software , Interface Usuário-Computador , Sequência de Aminoácidos , Documentação/métodos , Dados de Sequência Molecular , Proteínas/análise , Proteínas/classificaçãoRESUMO
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.
Assuntos
Biologia Computacional , Internet , Software , Bases de Dados Factuais , Interface Usuário-ComputadorRESUMO
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.
Assuntos
Motivos de Aminoácidos , Bases de Dados Factuais , Conformação Proteica , Proteínas , Internet , Estrutura Terciária de Proteína , Proteínas/química , Proteínas/genética , SoftwareRESUMO
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. In this publication we have identified SAND in diverse eukaryotes, from single celled organisms such as the yeasts to complex multi-cellular chordates such as mammals. We have demonstrated subfamily divisions in the SAND proteins and show that in vertebrates, a duplication event gave rise to two SAND sequences. This duplication appears to have occurred during early vertebrate evolution and conceivably with the evolution of lysosomes. Using bioinformatics we predict a secondary structure, solvent accessibility profile and protein fold for the SAND proteins and determine conserved sequence motifs, present in all SAND proteins and those that are specific to subsets. A comprehensive evaluation of yeast and human functional studies in conjunction with our in silico analysis has identified potential roles for some of these motifs.
