WWU Münster UKM
"Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum" by Runtuwene at al. has been published by Scientific Reports
Welcome Marten Kellner at our institute!
Welcome Felix Manske at our institute!
Ein- und Ausschalter der Gene: Muensters Wissenschaftler entdecken neue Form der Transkription zur Genregulation
"Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis" Shabardina et al. has been published by Int. J. Biol. Sci.
"Loss-of-function uORF mutations in human malignancies" by Schulz et al. has been published by Scientific Reports
Welcome Jonas Bohn to our institute!
"Transcriptional interference by small transcripts in proximal promoter regions" by Pande et al. has been published by Nucleic Acids Research.

Visualizing Sequence Similarity of Protein Families

Classification of proteins into families is one of the main goals of functional analysis. Proteins are usually assigned to a family on the basis of the presence of family-specific patterns, domains, or structural elements. Whereas proteins belonging to the same family are generally similar to each other, the extent of similarity varies widely across families. Some families are characterized by short, well-defined motifs, whereas others contain longer, less-specific motifs. We present a simple method for visualizing such differences. We applied our method to the Arabidopsis thaliana families listed at The Arabidopsis Information Resource (TAIR) Web site and for 76% of the nontrivial families (families with more than one member), our method identifies simple similarity measures that are necessary and sufficient to cluster members of the family together. Our visualization method can be used as part of an annotation pipeline to identify potentially incorrectly defined families. We also describe how our method can be extended to identify novel families and to assign unclassified proteins into known families.

One result of our work is the discovery that, despite the wide variety of methods used in the construction of protein families, 76% of all analyzed Arabidopsis thaliana families are fully clusterable by the proposed simple parameter schemes. Our results also show relationships between families that shar/ members, and help identify potentially incorrect family assignments. We also show how our results could be used to identify novel families and assign unclassified proteins to known families.

Reference: Veeramachaneni V. and Makalowski W. (2004) Visualizing sequence similarity of protein families. Genome Research, 14 (6): 1160-1169.[Reprint]
2012-11-19 14:06