To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported ... MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a ... This allows an interactive assessment of the distribution of gene functions in the environment. MetaLook allows scientists to ... centralised georeferenced database. The user can define environmental containers to organise the sequences according to ...

PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in ... We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how ... Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with ... these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein ...

... extended options to handle protein kinase and substrate data and an improved web interface. The new features significantly ... Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase ... sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining ... We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The ...

... gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences ... but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains ... VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed ... Sequence databases usually use HTML pages to mediate remote sorting, ...

It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting ... As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene ... evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www. ... and send resulting annotations to external curation databases. ... by the zyg-1 gene which encodes a protein with sequence ...

In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper ... Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and ... that does not negatively affect the performance of large-scale search in protein sequences. ... In this work, we consider comparisons between a set of protein queries against a large protein database of N amino acids. A ...

... enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface ... In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. ... thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput ... PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single ...

... many proteins are ignored by the currently available databases of cognate proteins, despite the high amount of important genes ... Typically, databases of related proteins focus on those from completely-sequenced genomes. Unfortunately, relatively few ... It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, ... We have developed a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through ...

Most proteins perform their functions by interacting with other proteins, so predicting PPIs accurately is crucial for ... In our paper, we use GCNs to learn the position information of proteins in the PPIs networks graph, which can reflect the ... In previous research methods, most of them only used protein amino acid sequence as input information to make predictions, ... We first time combine amino acid sequence information and position information to make representations for proteins. The ...

We propose a RDF model, GORouter, which encodes heterogeneous original data in a uniform RDF format, creates additional ... is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the ... which can only be used to annotate genes and gene products of the Saccharomyces Genome Database (SGD). These species-specific ... that fetch gene products of Rat Genome Database (RGD) associated with MF protein dimerization activity (GO:0046983) and CC ...

The system is then tested using a subset of Saccharomyces cerevisiae Protein-Protein interaction dataset. We used this subset ... in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed ... Of course experimentalists can take advantage of using different online databases containing a list of PPIs for each species ( ... the biological significance of each protein complexes is validated by means of the Gene Ontology Term Finder web service [45], ...

Rudd S, Tetko IV: Eclair-a web service for unravelling species origin of sequences sampled from mixed host interfaces. Nucleic ... Pearson WR: Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol 1994, 24: 307-331. ... Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268: 78-94. 10.1006/jmbi. ... For instance, some applications use lower- and uppercase characters in the raw sequence to encode additional annotations in ...

... and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab. ... transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to ... Spivak AT, Stormo GD: ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. ... MotifLabs graphical user interface. The screenshot shows MotifLabs graphical user interface with three data panels to the ...

In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include ... With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 ... Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy ... The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the ...

However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due ... Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein-protein ... Instead of using hand-crafted protein features, we utilize statistically rich protein representations learned by a deep ... Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein ...

... we were able to explore the highest-ranking cluster and determine that it represents a strong contender for proteins working ... Combining this dataset with the yeast protein-protein interaction network from STRING, we were able to perform a variety of ... protein query as the Data Source and Saccharomyces cerevisiae as the species. Then select "All proteins of this species" and ... First, the proteins in the cluster were manually looked up in the protein database UniProt [59]. Furthermore, functional ...

In this work, we present a new approach to study the cooperation of functional modules (sets of functionally related genes) in ... Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential ... A cooperative module pair is defined as two modules that significantly cooperate with certain functional genes in a cellular ... We found that 14, 36, 18, 15, and 20 cooperative module pairs significantly cooperate with genes regulated in early G1, late G1 ...