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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 leucine zipper is a dimerisation domain occurring mostly in regulatory and thus in many oncogenic proteins. 2ZIP combines a standard coiled coil prediction algorithm with an approximate search for the characteristic leucine repeat. No further information from homologues is required for prediction. This approach improves significantly over existing methods, especially in that the coiled coil prediction turns out to be highly informative and avoids large numbers of false positives
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The 3of5 application aims at the analysis of protein sequences to find user-defined patterns, described via complex regular expressions-like terms, e.g. to search for a motif with 3 basic AAs in 5 positions.
keywords: regular expression
Categories: proteomics, (protein sequences and identification, proteomics experiment) - Software type(s): website - tool
Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Categories: proteomics, (function analysis) - Software type(s): website - tool
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies, developed by the Geneva Antibody Facility at the University of Geneva.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. Keep in mind that Agadir is not a program to predict secondary structure of proteins.
keywords: alpha helix
Categories: proteomics, genomics, evolutionary biology - Software type(s): website, CLI - tool
ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Four tools for multiple alignments.
Categories: - Software type(s): - tool
ANOLEA (Atomic Non-Local Environment Assessment) is a server that performs energy calculations on a protein chain, evaluating the "Non-Local Environment" of each heavy atom in the molecule. The energy of each pairwise interaction is taken from a distance-dependent knowledge-based mean force potential that has been derived from a database of 147 non-redundant protein chains with a sequence identity below 25% and solved by X-Ray crystallography with a resolution lower than 3 A.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Advanced Protein Secondary Structure Prediction Server
Categories: population genetics - Software type(s): CLI, GUI - tool
Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options.
Categories: genomics, systems biology - Software type(s): website, CLI, library - database/tool
arrayMap is a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
Ascalaph is a general purpose molecular modeling software that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly).
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
Categories: genomics, evolutionary biology, population genetics - Software type(s): CLI, GUI - tool
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
Categories: evolutionary biology, transcriptomics - Software type(s): website - database
Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
GPI modification site prediction
Categories: proteomics, (function analysis), systems biology - Software type(s): website - tool
Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available.
Categories: evolutionary biology - Software type(s): website - tool
Neighbor Joining (NJ) algorithm improved for molecular sequences
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs
keywords: sequence alignment
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