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Showing 20 records out of 372 total
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Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The Simple Modular Architecture Research Tool allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. Normal SMART, (against UniProtKB and stable Ensembl proteomes), and Genomic SMART, (against complete proteomes) are supported.
keywords: protein domain
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
LC-MSMS software for small molecule identification, can search both low and high mass precision libraries. Users can search on multiple libraries simultaneously, including privately built ones.
Categories: genomics - Software type(s): website - database/tool
The resource is based on a new 'in silico' approach for identifying regulatory variants. The transcription factor (TF) binding score is computed in both the reference (hg19) and alternate human genome assemblies. The alternate genome assembly is generated by incorporating the alternate allele of common genetic variants (AF>=0.001) from the 1000 Genomes Project. Interesting candidate variants are those SNPs that disrupt, create or change the TF binding score/affinity between the two genomes.
Categories: IT infrastructure - Software type(s): website, CLI - tool
Web services interface to bioinformatics tools
keywords: Taverna
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary structure prediction.
Categories: proteomics, (function analysis, protein modifications) - Software type(s): website - tool
Classification and secondary structure srediction of membrane proteins.
Categories: proteomics, IT infrastructure - Software type(s): website - tool
SPARQL playground aims to help newbies to get started with SPARQL. It provides a user friendly interface with a simple dataset and examples.
keywords: network
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
SSA is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site. The programs provided by this web server are the following: generation of a constraint profile (Cpr); generation of a signal list (SList); generation of a signal occurrence profile (OProf); pattern optimization tool (PatOp); find motifs around functional sites (FindM), and extract sequences around functional sites (FromFPS).
Categories: systems biology - Software type(s): website - tool
Short Tandem Repeat (STR) analysis is one of the most useful methods in molecular biology which is used to compare specific loci on DNA from two or more samples. A short tandem repeat (STR or microsatellite) is a pattern of two or more nucleotides that are repeated directly adjacent to each other. Search for similarities between your cell line samples and the STR profiles in human cell lines stored in the Cellosaurus knowledgebase for cell lines.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Java-based software for structural alignments of proteins
keywords: sequence alignment
Categories: proteomics, (protein interactions) - Software type(s): website - database
STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.
keywords: network
Categories: glycomics - Software type(s): website - database
SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.
Categories: glycomics - Software type(s): website - tool
SugarSketcher was designed to provide users with a simple and efficient interface for drawing glycan molecules with the logos defined in the Symbol Nomenclature for Glycans (SNFG) . The tool operates in a quick mode in which the top menu shows a limited set of logos or in a normal mode in which the top menu is comprehensive. In either cases, a structure can be drawn from scratch or from a core structure. Structures are exportable as .svg images or in the GlycoCT format.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well as sulfated tyrosines clustered within 25 amino acid windows, respectively. All four HMMs contain the distilled information from one multiple sequence alignment.
Categories: proteomics - Software type(s): website - tool
SulfoSite is to computationally predict sulfation sites within given protein sequences. A representative set of 162 protein tyrosine sulfation sites from the Swiss-Port were used to analyze characteristics and to train and test in SulfoSite. Support Vector Machine (SVM) is applied for learning to each group of sequences and accessible surface area (ASA) value surrounding to the sulfation residues.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The SUMOplot??? Analysis Program predicts and scores sumoylation sites in your protein. The presence of this post-translational modification may help explain larger MWs than expected on SDS gels due to attachment of SUMO protein (11kDa) at multiple positions in your protein.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Protein sumoylation plays important roles in a variety of biological processes, such as transcriptional regulation, signaling transduction, cell cycle progression and differentiation. SUMOsp predicts sumoylation sites in proteins.
Categories: sequence sites, features and motifs - Software type(s): website - tool
Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Use the SUPERFAMILY database of structural and functional annotation to provide structural (and hence implied functional) assignments to protein sequences primarily at the SCOP superfamily level. A superfamily contains all proteins for which there is structural evidence of a common evolutionary ancestor. This service offers sophisticated and expertly chosen remote homology detection.
Categories: evolutionary biology - Software type(s): GUI - tool
SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms
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