UniqueProt: creating representative protein sequence sets
نویسندگان
چکیده
منابع مشابه
UniqueProt: creating representative protein sequence sets
UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences. The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity. UniqueProt is not a real clustering program in the sense that the 'representatives' are not at the centres of well-defined clus...
متن کاملSelection of representative protein data sets.
The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to ex...
متن کاملRepresentative Protein Sequence and Structure Database
The database provides the information about the non-redundant protein dataset (1573 proteins) obtained from the Protein Data Bank. The information includes PDB ID, Length of the protein, Resolution, PDB Secondary structure, PDB secondary structure summary, PHD secondary structure prediction, PHD secondary structure prediction summary, sequence. We further revised the PDB Secondary structure sum...
متن کاملSelecting Representative Data Sets
A training set is a special set of labeled data providing known information that is used in the supervised learning to build a classification or regression model. We can imagine each training instance as a feature vector together with an appropriate output value (label, class identifier). A supervised learning algorithm deduces a classification or regression function from the given training set...
متن کاملRSDB: representative protein sequence databases have high information content
MOTIVATION Biological sequence databases are highly redundant for two main reasons: 1. various databanks keep redundant sequences with many identical and nearly identical sequences 2. natural sequences often have high sequence identities due to gene duplication. We wanted to know how many sequences can be removed before the databases start losing homology information. Can a database of sequence...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2003
ISSN: 1362-4962
DOI: 10.1093/nar/gkg620