Welcome to the Bioinformatics Toolkit

The Bioinformatics Toolkit is a platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house and several public tools are offered with extended functionality.

If you find our Toolkit useful for your research, please cite us:
Alva V., Nam SZ., Söding J., Lupas AN. (2016) The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res.

 

Tool Map

 
 
 
6FrameTranslation
Six-frame translation of nucleotide sequences
Ali2D
Plots info on secondary structure and transmembrane regions onto a MSA
AlignmentViewer
Alignment viewer with BioJS MSA viewer
Aln2Plot
Shows a graphical overview of hydrophobicity and side chain volume
ANCESCON
Reconstructs ancestral protein sequences
Backtranslator
Reverse translation of amino acid into nucleotide sequences
bFit
Probabilistic method for robust superposition and comparison of protein structures
Blammer
Coverts BLAST/PSI-BLAST results to MSAs
BLASTClust
Ciusters sequences by single-linkage clustering
CLANS
Clustering based on all-against-all BLAST similarities
ClubSub-P
Database of cluster-based subcellular localization predictions for Archaea and Gram-negative bacteria
Clustal Omega
Multiple sequence alignment tool
COILS/PCOILS
Precition of coiled coils
CS-BLAST
Sensitive sequence comparison tool
daTAA
Annotation of domain in trimeric autotransporter adhesins
FRpred
Prediction of functional residues in multiple sequence alignments
GCView
Displays the genomic context of protein coding genes found in sequence searches
GI2Promoter
Extraction of nucleotide sequences upstream of given genes
GLProbs
Multiple sequence alignment tool
HHalign
Aligns two alignments with each other by pairwise alignment of HMMs
HHblits
Remote homology detection method based on iterative HMM-HMM comparison
HHcluster
Explore sequence relationships in protein fold space
HHfilter
Extraction of a representative set of sequences from an alignment
HHfrag
Builds a customized library of structural fragments
HHomp
Detection and classification of outer membrane proteins
HHpred
Homology detection & structure prediction by HMM-HMM comparison
HHrep
de novo identification of repeats
HHrepID
de novo identification of repeats
HHsenser
Sensitive intermediate profile search using HMM-HMM comparison
HMMER3
Sensitive sequence searching based on profile HMMs
Kalign
Multiple sequence alignment tool
MAFFT
Multiple sequence alignment tool
MARCOIL
Prediction of coiled coils based on HMMs
Modeller
Comparative protein structure modelling by satisfaction of spatial restraints
MSAProbs
Multiple sequence alignment tool
MUSCLE
Multiple sequence alignment tool
PatternSearch
Search based on PROSITE pattern/regular expression
ProbCons
Multiple sequence alignment tool
ProtBLAST+
NCBI BLAST+
PSI-BLAST+
NCBI PSI-BLAST+
Quick2D
Overview of secondary structure features like coiled coils, transmembrane helices and disordered regions
Reformat
Sequence reformatting utility
REPPER
Detects short gapless repeats
RetrieveSeq
Sequence retrieval using a list of GI numbers
SamCC
Measures structural parameters of four-helical bundles
SimShiftDB
Alignments based on chemical shifts
TCoffee
Multiple sequence alignment tool
TPRpred
Detects Tetratrico Peptide Repeats (TPRs), Pentatrico Peptide Repeats(PPRs) and SEL1-like repeats
ExtractGIs
Extraction of GI numbers
PHYLIP-NEIGHBOR
Infer phylogenies
HHpred
Homology detection & structure prediction by HMM-HMM comparison
PDBalert
Alerts users as soon as a pdb structure with homology to a protein of interest becomes available

 

Recent Updates

December, 2016

We are currently refactoring our tools to use NCBI accession.version identifiers instead of GI (see announcement from NCBI).

November, 2016

HHblits: we now offer HHblits v3.0.0 and the new Uniclust30 database.

October, 2016

We no longer offer legacy BLAST tools ProtBLAST and PSI-BLAST. Please use ProtBLAST+ and PSI-BLAST+ instead.

July, 2016

PfamA 30.0 and CDD 3.15 are now available for HHpred.

June, 2016

We now offer the nr50 database with many different tools (e.g. HMMER3, ProtBLAST+, CLANS).

May, 2016

Our new manuscript on the Toolkit has been published in Nucleic Acids Research.

February, 2016

PfamA 29.0 database is now also available for HHpred.

January, 2016

BLAST+ has been updated to version 2.3.0 and MODELLER to version 9.16. FRpred uses the BioJS Tree Viewer for displaying UPGMA dendrograms and the multiple sequence alignment tool GLProbs has been added to our alignment section.

HHpred bugfix: probability cut-off is working again. New PatternSearch feature: found patterns are highlighted also in the export file.

December, 2015

ANCESCON and AlignmentViewer now use the BioJS Tree Viewer and the BioJS MSA Viewer instead of the Archaeopteryx Tree Viewer applet and instead of the JalView applet, respectively. Now, these tools are also fully functional in the Chrome browser.

PSI-BLAST+ and ProtBLAST+ now use BLAST+ 2.2.31.

August, 2015

HMMER3 now uses hmmer 3.1b2 instead of hmmer 3.0.

Added new tools PSI-BLAST+ and ProtBLAST+, which are similar to tools PSI-BLAST and ProtBLAST, respectively. The new tools use BLAST+ programs, while tools PSI-BLAST and ProtBLAST continue to use legacy BLAST.

July, 2015

MAFFT, TCoffee, Modeller, Muscle, and Phylip-Neighbor were updated to their latest versions.

May, 2015

To improve the user experience of our toolkit in browsers not supporting Java applets, the tools Modeller and bFit now use JSmol for displaying PDB structures.

November, 2014

SCOP 1.75 databases were replaced by SCOPe 2.04 databases.

June, 2013

The signal peptide identification protocol Predisi has been added to Quick2D.

April, 2013

The sequence alignment tool MSAProbs has been added to our library of programs.

April, 2013

Clustal Omega has been made default for the Clustal alignment protocol.

 


Most frequently used tools

HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3D homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHpred software is part of the open source package HHsuite.

HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite.

Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2.

Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints.

Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation.

PSI-BLAST+ Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST+ but more sensitive. PSI-BLAST+ first performs a BLAST+ search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.

To find a tool not listed here, choose the appropriate section tab above, or look for the tool in the Quickfinder on the top right corner.


Job submission

Each tool has a separate input page with a web form in which the user can input sequence data, upload sequence files, and specify options. All tools that take alignments as input accept the most widely used formats (FASTA, CLUSTAL, Stockholm and A3M). You may also choose your own job-names to organize your work. Snail symbols inside the submit buttons inform you about tools that typically run for more than 10 minutes.

If you plan to use the toolkit extensively (more than about 50 jobs per day), please consider installing and running the corresponding bioinformatics programs on your own hardware or inform us before (see Contact). If you inform us, we can tell you about internal events which require high availability of the toolkit resources. If the load gets too high, we may block ip addresses temporarily from accessing the toolkit and even may terminate running jobs.

 

Job management

Located on the left of the screen is a sidebar pane that holds a status and section-coded list of all recent jobs in the current session. You can click on previously submitted jobs to check their status and view their results.
In general a session will last until the web browser is closed. However, because of different session implementations by the various browser types, jobs may occasionally disappear from the joblist. Therefore, noting down the job ids is recommended. Anonymous job results are stored two weeks, whereas jobs of logged-in users are stored at least two months.

Please keep in mind, that the toolkit is focussed on providing tools, not on storing results or other data: We don't backup of your results. If the storage medium crashes or your job is deleted, we cannot restore it! After removal or updates of databases or tools, you probably will not be able to get the same results any more, even if you still know your input parameters. It's your task to save your results and databases.

 

Interconnectivity

Most of the tools in the Toolkit are interconnected, allowing job results of one tool to be forwarded as input to others. For example, you could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool.

 

User databases

You may upload customized databases which are then accessible throughout the whole toolkit (upload once, use many times).