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Showing 20 records out of 363 total
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Categories: proteomics, (function analysis) - Software type(s): website - tool
GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest.
GPS
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Computational prediction of phosphorylation sites with their cognate protein kinases (PKs) is greatly helpful for further experimental design. GPS could predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy.
Categories: protein sequences and identification, genomics - Software type(s): website - tool
Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values
Categories: proteomics, (protein sequences and identification, function analysis, sequence sites, features and motifs) - Software type(s): website - database/tool
HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.
Categories: proteomics - Software type(s): website - tool
The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
HeliQuest calculates from the amino acid sequence of a helix (??-helix, 3-10 helix, 3-11 helix or ?? helix) its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Homology detection & structure prediction by HMM-HMM comparison
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Prediction of transmembranes helices and topology of proteins.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Helical TransMembrane Segment Rotational Angle Prediction
Categories: proteomics, (proteomics experiment), imaging - Software type(s): website, GUI - tool
Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
InsPecT is an MS/MS database search tool, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, InsPecT implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.
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.
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