Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
نویسندگان
چکیده
منابع مشابه
SISYPHUS—structural alignments for proteins with non-trivial relationships
With the increasing amount of structural data, the number of homologous protein structures bearing topological irregularities is steadily growing. These include proteins with circular permutations, segment-swapping, context-dependent folding or chameleon sequences that can adopt alternative secondary structures. Their non-trivial structural relationships are readily identified during expert ana...
متن کاملApproaches to detection of distantly related proteins by database searches.
The searching of protein databases as a method of identifying newly sequenced genes is commonplace in molecular biology laboratories. However, it is a procedure that is not usually formally taught to students, and method cookbooks discuss it only briefly. This article uses a single family of highly diverged uracil-DNA glycosylases, which fall into two distinct groups, to highlight some of the d...
متن کاملUsing Hybrid Alignment for Iterative Sequence Database Searches
Progressive sequence model refinement by means of iterative searches is an effective technique for high sensitivity database searches and is currently employed in popular tools such as PSI-BLAST and SAM. Recently, a novel alignment algorithm has been proposed that offers features expected to improve the sensitivity of such iterative approaches, specifically a well-characterized theory of its st...
متن کاملDatabase tool SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation
Bologna Biocomputing Group, University of Bologna, via S. Giacomo 9/2, I-40126, Bologna, Italy, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, via Selmi 3, I-40126, Bologna, Italy, Department of Computer Science and Engineering, University of Bologna, Mura A. Zamboni 7, I-40126, Bologna, Italy, Health Science and Technologies-ICIR, University of ...
متن کاملNew structural variation in evolutionary searches of RNA neutral networks
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets of RNA sequences that fold into the same structure. Our work extends and deepens previous studies on neutral networks. First, we show that even the 1-mutant ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Molecular Biology
سال: 1999
ISSN: 0022-2836
DOI: 10.1006/jmbi.1999.2653