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Showing 20 records out of 369 total
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Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw.
Categories: genomics - Software type(s): website, CLI - tool
TagScan allows searching for exact or near-exact matches between oligonucleotide queries of up to 60 bases and sequence databases comprising entire genomes or mRNA reference sequences. The smallest query allowed is 10 nucleotides long.
Categories: proteomics, (function analysis, protein modifications) - Software type(s): website - tool
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).
Categories: proteomics, (protein modifications) - Software type(s): website - tool
TatP 1.0 server predicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of two artificial neural networks. A postfiltering of the output based on regular expressions is possible.
Categories: proteomics, (protein interactions), systems biology - Software type(s): website - database
Database show prediction of interaction specificity in two-component systems. These predictions were made with new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains.
keywords:
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Pattern discovery on event streams of alphanumeric characters. Possible alphabet sets include nucleic acids, amino acids, etc.
keywords: protein domain
Categories: proteomics, (protein modifications) - Software type(s): website - tool
TermiNator predicts N-terminal methionine excision, N-terminal acetylation, N-terminal myristoylation and S-palmitoylation of either prokaryotic or eukaryotic proteins originating from organellar or nuclear genomes. It also relates the predicted N-terminus to protein half-life (5-220 hours) and relative translation efficiency (relative value 1-5) of eukaryotic proteins.
Categories: proteomics, (protein modifications) - Software type(s): website, API - tool
N-Terminal Acetylation and initial methionine predictor based on patterns discovery and decision trees. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high-performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and Nα-terminal acetylation (N-Ac), two of the most common PTMs.
Categories: transcriptomics - Software type(s): website - tool
A package of bioinformatics tools for data analysis, mainly for microarrays
keywords: conversion tool
Categories: evolutionary biology - Software type(s): website - tool
The PhylOgenetic Web Repeater (POWER) allows users performing phylogenetic analysis with molecular data by most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the begining of the pipeline whereas the other begin phylogenetic analysis with aligned sequence.
Categories: systems biology - Software type(s): CLI, GUI - tool
An easy-to-use open source software package and API for systems biologists. It performs multiple analyses on stoichiometric reaction networks and other biological networks, and can be easily extended via a number of plugins.
keywords: metabolism, network
Categories: proteomics - Software type(s): website - tool
Three to One converts three letter translations to single letter translations
Categories: proteomics - Software type(s): website - tool
This tool can convert 3-letter amino acid codes to 1-letter amino acid codes and inversely.
Categories: proteomics, (protein structure) - Software type(s): website - tool
TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
TMHMM is a membrane protein topology prediction method based on a hidden Markov model (HMM). It predicts transmembrane helices in proteins.
Categories: proteomics, (protein structure) - Software type(s): website, CLI - tool
The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins
Categories: proteomics, (protein structure) - Software type(s): website - tool
Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Topology prediction of membrane proteins
Categories: proteomics, (protein structure) - Software type(s): website - tool
TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units.
Categories: proteomics, (protein sequences and identification), genomics, transcriptomics - Software type(s): website - tool
Translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
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