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Showing 20 records out of 369 total
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Categories: proteomics, (function analysis) - Software type(s): website - tool
Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature.
Categories: proteomics, (protein structure) - Software type(s): website - tool
The PSIPRED Protein Structure Prediction Server aggregates several of our structure prediction methods into one location. Users can submit a protein sequence, perform the prediction of their choice and receive the results of the prediction via e-mail.
Categories: proteomics, (function analysis) - Software type(s): website - tool
PSORT family of programs for subcellular localization prediction
Categories: proteomics, (protein modifications) - Software type(s): website - tool
predict peroxisomal targeting signal 1 containing proteins
Categories: similarity search/alignment - Software type(s): website - tool
This server calculates the protein sequence variability within a multiple sequence alignment using several variability metrics. Subsequently, the server can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure.
keywords: alignment analysis
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
PyMOL is a user-sponsored molecular visualization system on an open-source foundation.
Categories: proteomics, (protein structure), structure analysis, biophysics - Software type(s): website - tool
Estimating the quality of predicted structural models is a crucial step in homology modeling. Scoring functions analyze different structural features of the protein models in order to generate a quality estimate. QMEAN consists of four statistical potential terms (two non-bonded interaction terms, a torsion angle term and a solvation term) and two components describing the agreement between predicted and observed secondary structure and solvent accessibility.
Categories: genomics, transcriptomics - Software type(s): library - tool
QuasR: R/Bioconductor package for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.
Categories: proteomics, (proteomics experiment, protein modifications) - Software type(s): CLI, GUI - tool
QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.
Categories: proteomics - Software type(s): website - tool
Random protein sequence generator
Categories: proteomics - Software type(s): website - tool
This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
RasMol is a program for molecular graphics visualization.
Categories: proteomics, evolutionary biology - Software type(s): website - tool
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package.
Categories: structure analysis - Software type(s): website - tool
rBAN (retroBiosynthetic Analysis of Nonribosomal peptides) is a computational tool designed to predict the monomeric graph of NRPs from their atomic structure in SMILES format. This prediction is achieved through the in-silico fragmentation of a chemical structure and matching the resulting fragments against the monomers of Norine for identification.
Categories: evolutionary biology - Software type(s): website, CLI - tool
REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites will be available for download after the analysis is finished.
REP
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Protein search for repeats, using a collection of repeat families
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
REPRO is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.
Categories: proteomics, genomics - Software type(s): website - tool
This tool converts DNA to RNA to protein, and reverse transcript RNA to DNA.
keywords: translation
Categories: protein sequences and identification, genomics - Software type(s): website - tool
Accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence representing the most likely non-degenerate coding sequence. A consensus sequence derived from all the possible codons for each amino acid is also returned.
keywords: translation
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