Gene and protein analysis programs and databases
Last modified: June 19, 2008
- AMAS -
Analyse Multiply Aligned Sequences
- BLOCK Maker (protein
homology blocks)
- CLUSTALW
- CLUSTALW and CLUSTALX
- Download
- CINEMA -
Viewer for aligned sequences
- Jalview - a multiple alignment
editor written in
Java.
- MEME & MAST (motif search
and alignment)
- Match-Box
- multiple protein sequence alignment based on strict statistical criteria.
- MUSCLE
- Multiple sequence comparison by log-expectation.
- PipeAlign PipeAlign is an on-line protein family analysis tool providing both interactive
and automatic workbench for the validation, integration and presentation of the
biological insights resulting from the analysis.
- PRALINE -
multiple sequence alignment with many options (e.g. global or local
preprocessing, predicted secondary structure information and iteration
capabilities) to optimise the information for each of the input sequences.
- ProbCons - an efficient
protein multiple sequence alignment program, which has demonstrated a
statistically significant improvement in accuracy compared to several
leading alignment tools.
- T-Coffee - a multiple
sequence alignment program that will allow you to combine results obtained
with several alignment methods.
Prediction of Protein Subcellular Location
- ChloroP - Prediction
of N-terminal chloroplast transit peptide, and, if predicted, the probable
site for cleavage of the transit peptide.
- Golgi
Predictor - Prediction of Golgi Type II membrane proteins based on
their transmembrane domains
- Locate - A Protein Subcellular
Localization Database
- LocSVMpsi
- protein subcellular LOCalization based on SVM and PSI-blast v.1.3
- MITOPROT - Prediction of
mitochondrial targeting sequences
- PredictNLS - an automated tool for the analysis and determination of Nuclear Localization
Signals (NLS).
- Predotar - Prediction of
mitochondrial and plastid targeting sequences
- PTS1
- Prediction of peroxisomal targeting signal 1 containing proteins
- SecretomeP -
The SecretomeP 1.0b server produces ab initio predictions of non-classical
i.e. not signal peptide triggered protein secretion in eukaryotes.
- SignalP Server -
Predictions of the presence and location of signal peptide cleavage sites in
amino acid sequences from prokaryotes and eukaryotes.
- TargetP - TargetP predicts the subcellular location of eukaryotic protein sequences and the potential cleavage site for sequences predicted to contain
a chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or
secretory pathway signal peptide (SP).
General Protein Motif Resources
- DeltaMass - A Database of Protein Post Translational
Modifications
- ELM - Eukaryotic linear motif resource for functional sites in proteins
- Prosite - Database of protein families and domains including functional patterns
- Resid - comprehensive
collection of annotations and structures for protein modifications including
amino-terminal, carboxyl-terminal and peptide chain cross-link
post-translational modifications.
- QuasiMotiFinder - A server
for the identification of signatures and signature-like patterns in protein
sequences
- ScanMot -
searching for similar sequences using a simultaneous scan of multiple
sequence motifs.
Specialized Protein Motif Resources
- Big-PI predictor -
GPI modification site prediction.
- CANSITE - Scan your protein for
potential signaling effector and adaptor sites
- CSS-Palm - in
silico prediction of palmitoylation sites
-
DictyOGlyc 1.1
Server - Predictions of GlcNAc O-glycosylation sites in Dictyostelium
discoideum proteins.
- GPI-SOM - Identification of GPI-anchor
signals by a Kohonen Self Organizing Map
- GPS
- Group-based phosphorylation scoring method
- KinasePhos - Prediction of
protein phosphorylation
sites.
- Myristoylator - Prediction of N-terminal myristoylation by neural networks
- NetAcet - Prediction
of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
- NetOGlyc 2.0 Server
- Predictions of mucin type GalNAc O-glycosylation sites in human proteins.
- NetNES - neural network
predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins
using a combination of neural networks and hidden Markov models.
- NetNGlyc 1.0 Server
- Predictions of N-glycosylation sites in mammalian proteins.
- NetPhos - neural network predictions for serine, threonine and tyrosine phosphorylation
sites in eukaryotic proteins.
- NetPhosK - neural network predictions
of kinase specific eukaryotic protein phosphorylation
sites.
- NMT - The MYR predictor -
Predicts N-terminal N-Myristoylation of Proteins.
- PhosphoELM - A
database of phosphorylation sites with a phosphorylation prediction program.
- Sulfinator -
Predicts tyrosine sulfation sites in protein sequences.
- SUMOplot - Prediction of
SUMO protein attachment sites
- SIFT - Predictions of amino acid substitutions on protein function
- YinOYang
- neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein
sequences.
- DictyOGlyc 1.1
Server - Predictions of GlcNAc O-glycosylation sites in Dictyostelium
discoideum proteins.
- OGlycbase
- O-glycosylated protein database.
- Biomolecular InteractioN Database - full descriptions of
interactions, molecular complexes and pathways.
- DIP - Database of Interacting
Proteins.
- HPID - Human Protein
Interaction Database
- MINT - Molecular INTeraction database.
- OPHID - The Online Predicted
Human Interaction Database.
- PIP - Potential Interactions
of Proteins
- PRISM - PRotein
Interactions by Structural Matching (v 0.93)
If you have any comments or suggestions be sure to let me know!
Peter Taschner - P.Taschner@lumc.nl