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Showing 20 records out of 359 total
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Categories: proteomics, (protein modifications) - Software type(s): website, API - tool
PTMs 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.
Categories: genomics, (characterisation/annotation), population genetics - Software type(s): GUI - tool
TRiFLe is a program for simulating TRFs and identifying species by TRF profiling
keywords:
Categories: genomics, (characterisation/annotation), transcriptomics - Software type(s): website, CLI - tool
The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
TRUST is a method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments.
Categories: proteomics, glycomics - Software type(s): website - database
UniCarb-DB stores data and information on glycan structures and associated fragment data characterised by LC-MS/MS strategies. It is annotated with high-quality datasets.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - database
UniCarbKB is a curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures. It includes data previously available from GlycoSuiteDB.
Categories: proteomics - Software type(s): website - database
UniParc is a comprehensive and non-redundant database provided by the UniProt Consortium that contains most of the publicly available protein sequences. Proteins may exist in different source databases and in multiple copies in the same database. UniParc avoids such redundancy by storing each unique sequence only once and giving it a stable and unique identifier allowing to identify the same protein from different source databases. UniParc contains only protein sequences.
keywords:
Categories: proteomics, (protein sequences and identification, function analysis, similarity search/alignment) - Software type(s): website - database
The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium and is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
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