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Showing 20 records out of 375 total
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Categories: proteomics, genomics, systems biology - Software type(s): website, databases files - database/tool
This is both a tool and a database. Via a web service, users can generate i) integrated proteogenomics databases (iPtgxDBs) that can be used to identify as of yet missing protein-coding genes in prokaryotic organisms, and ii) a GFF file that contains all integrated annotations from reference genome annotations, gene prediction softwares like Prodigal, and a modified 6-frame translation (considering alternative start codons). Users are encouraged to make their iPtgxDBs available.
Categories: transcriptomics - Software type(s): CLI - tool
The Iterative Signature Algorithm (ISA) was designed to reduce the complexity of very large sets of data by decomposing it into so-called "modules". In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different "resolutions" of the modular mapping.
Categories: genomics, (characterisation/annotation) - Software type(s): CLI, GUI - tool
A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.
keywords:
Categories: proteomics, (protein modifications), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - tool
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Categories: proteomics, (proteomics experiment), genomics, (characterisation/annotation) - Software type(s): website - tool
Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
Jmol is an open-source Java viewer for chemical structures in 3D.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction Server
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Kalign is a fast and accurate multiple sequence alignment algorithm.
keywords: sequence alignment
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Kalign is a fast and accurate multiple sequence alignment algorithm.
keywords: sequence alignment
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment, similarity search) - Software type(s): website, CLI - tool
LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The LipoP 1.0 server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and N-terminal membrane helices in Gram-negative bacteria, with a good performance on sequences from Gram-positive bacteria also.
Categories: - Software type(s): - tool
LiveBench provides simple evaluation of the structure prediction servers from the point of view of a potential user. The evaluation of sensitivity and specificity of the available servers can help the user develop sequence analysis strategies and assess the confidence of the obtained predictions.
Categories: genomics, (sequence alignment) - Software type(s): website, CLI - tool
MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Such data might consist of counts, probabilities, or intensities associated with genome positions. They may be generated by mapping mRNA 5' and 3' sequence tags to genomes, by ChIP-chip or ChIP-Seq assays, or by genome-wide genotype-phenotype association studies. MADAP identifies clusters of data points corresponding to genomic features.
keywords:
Categories: proteomics, (similarity search/alignment, sequence alignment) - Software type(s): website - tool
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
keywords: sequence alignment
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
keywords: sequence alignment
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.
Categories: proteomics, (protein structure, protein interactions) - Software type(s): website - tool
Macromolecular structure pdb files that represent multimeric molecules often do not contain the coordinates of all multimer subunits. For such files, MakeMultimer.py calculates the coordinates of the missing subunits from the BIOMT transformation matrices contained in the pdb file.
Categories: proteomics, (proteomics experiment) - Software type(s): website, GUI - tool
A tool to quantify MALDI peptides (SILAC) from Phenyx output
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
C++ program for HMM models
Categories: proteomics, (protein structure), structure analysis - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
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