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Showing 20 records out of 359 total
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Categories: evolutionary biology - Software type(s): website - database
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - tool
Seq2Logo is a web-based sequence logo method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - tool
SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualize sequence patterns and represent a more informative alternative to consensus sequence
Categories: proteomics, genomics, (characterisation/annotation) - Software type(s): website - tool
A data mining solution to map thousands of viral isolates (influenza, dengue and FMDV virus).
keywords:
Categories: similarity search/alignment - Software type(s): website - tool
This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function.
keywords: alignment analysis
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis.
Categories: proteomics, genomics - Software type(s): website - tool
SHOPS (SHow OPeron Structures) was developed to analyze the genomic operon context for any group of proteins selected on the basis of a set of sequence or domain identifiers. It uses genome annotations of all available fully sequenced prokaryotes to create a scaled graphical overview of the genomic context around the proteins of interest.
Categories: genomics, (characterisation/annotation) - Software type(s): CLI - tool
Software to analyse deep-sequencing (NGS) data and reconstruct haplotypes in a genetically heterogeneous sample
Categories: genomics, (sequence alignment), transcriptomics - Software type(s): CLI - tool
SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence.
keywords: sequence alignment
Categories: proteomics, (protein modifications) - Software type(s): website, CLI - tool
SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments.
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: proteomics, (protein structure) - Software type(s): website - tool
Java-based software for structural alignments of proteins
keywords: sequence alignment
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