The MPI Bioinformatics Toolkit for protein sequence analysis

Abstract

The MPI Bioinformatics Toolkit for protein sequence analysis

 

Andreas Biegert^*, Christian Mayer, Michael Remmert, Johannes Söding and Andrei N. Lupas

Department of protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany

Nucleic Acids Research 2006 34(Web Server issue):W335-W339; doi:10.1093/nar/gkl217. 

 

Abstract

The MPI Bioinformatics Toolkit is an interactive web servicewhich offers access to a great variety of public and in-housebioinformatics tools. They are grouped into different sectionsthat support sequence searches, multiple alignment, secondaryand tertiary structure prediction and classification. Severalpublic tools are offered in customized versions that extendtheir functionality. For example, PSI-BLAST can be run againstregularly updated standard databases, customized user databasesor selectable sets of genomes. Another tool, Quick2D, integratesthe results of various secondary structure, transmembrane anddisorder prediction programs into one view. The Toolkit providesa friendly and intuitive user interface with an online helpfacility. As a key feature, various tools are interconnectedso that the results of one tool can be forwarded to other tools.One could run PSI-BLAST, parse out a multiple alignment of selectedhits and send the results to a cluster analysis tool. The Toolkitframework and the tools developed in-house will be packagedand freely available under the GNU Lesser General Public Licence(LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de.

Introduction

As this special issue shows, the number of public bioinformatictools and web servers is growing quickly. However, the wealthof powerful tools and servers is, in our opinion, only utilizedby a fraction of biologists who would be able to profit fromthem. Especially for non-experts it can be very time-consumingto find out which services exist, what they can or cannot do,how to use them and how to feed results from one service tothe next in the right format. This has spawned the developmentof two classes of servers. The first class, exemplified by PredictProtein(1), accepts a single sequence as input, runs a whole set ofstandard protein analysis tools and returns the bare, concatenatedresults in a single Email or Web page, requiring users to befamiliar with the tools and their output format. The secondclass offers a collection of web interfaces to local versionsof public bioinformatic tools. For instance, PAT (protein analysistoolkit) (2) facilitates the combination of different analysismethods by automating repetitive data processing tasks. However,its user interface and the lack of an integrated help systemmake PAT, suited primarily for users with biocomputing experience.Two further servers designed as toolboxes for sequence analysisare the Biology Workbench (3), which has not been updated forquite some time, and AnaBench (4), which is more geared towardanalysis of DNA data.

The primary aim in developing the MPI Bioinformatics Toolkitwas to offer a web service that is as easy to use as possibleand that integrates a selected set of most useful methods forthe analysis of protein sequences. From our own experience asusers of the toolkit, its main advantages are as follows:

• In-housetools: Several programs developed in our group areavailableonly through our toolkit, e.g. HHpred (5), HHrep (6),HHsenser(7), REPPER (8), CLANS (9) and Blammer (10) (see Table 1).
• Enhancedfunctionality of public tools: Many tools offer additionalfunctionalitycompared with the original public server (seetool descriptionsbelow).
• User databases: Users may upload customized databaseswhichare then accessible throughout the whole toolkit (uploadonce,use many times).
• Interconnectivity: Most of the toolsin the Toolkit are interconnected,allowing job results of onetool to be forwarded as input toothers.
• Streamlined, uniformuser interface: Input forms are kept assimple and self-explanatoryas possible with a uniform designand logic for all tools.
• Straightforwardnavigation: Tools are grouped into color-codedsections thatare easily accessible via tabs.
• Job management: A dedicatedjobs sidebar provides informationand quick access to all jobresults of the current session.
• Personal work space: Usersmay register and log in to gain accessto a personal work spacefeaturing long-term storage of jobs.

Web interface

Currently, 30 bioinformatics tools and utilities can be launchedfrom the MPI Bioinformatics Toolkit (Table 1). All tool sectionsare accessible from a tabbed menu bar located at the top ofthe page (Figure 1). Each tab reveals a submenu containing thesection-specific tools, an overview page with brief descriptionsfor each tool and a list of selected links. Located on the leftof the screen is a sidebar pane that holds a status and section-codedlist of all recent jobs in the current session. One can clickon previously submitted jobs to check their status and viewtheir results. Users can also choose their own job names toorganize their work. Each tool has a separate input page witha web form, in which the user can input sequence data, uploadsequence files, and specify options.

 

Tool sections

The search section contains popular search tools, such as NucleotideBLAST,ProteinBLAST (11), PSI-BLAST (12), and HMMER (13), as well asour in-house developments such as HHpred, HHsenser and PatternSearch.In comparison with the NCBI server, our BLAST tools offer greaterflexibility and functionality: searches can be run against uploadedpersonal databases or selectable sets of genomes (updated weeklyfrom NCBI and ENSEMBL), databases can be switched between PSI-BLASTruns, alignments can be extracted, viewed online or forwardedto other tools, and two graphs show matched regions and E-valuedistributions. The fastHMMER tool performs HMMER searches ofall standard sequence databases in 10% of the time by reducingthe database with one iteration of PSI-BLAST at a cut-off E-valueof 10 000. PatternSearch identifies sequences containing a user-definedProsite pattern or regular expression. HHpred is a new serverfor protein structure and function prediction (5). It takesa query sequence as input and searches user-selected databasesfor homologs with a new and very sensitive method based on pairwisecomparison of hidden Markov models (HMMs). Available databases,among others, are InterPro, CDD and an aligment database webuild from Protein Data Bank (PDB) sequences and which can beused for 3D structure prediction. HHsenser is a transitive searchmethod based on HMM-HMM comparison (7). This method utilizesa sequence as input and builds an alignment with as many nearor remote homologs as possible, often covering the whole proteinsuperfamily.

The alignment section includes the well-known, popular multiplealignment program ClustalW (14), together with the more recentlydeveloped multiple alignment methods ProbCons (15), MUSCLE (16)and MAFFT (17). Also in this section is Blammer (10), whichconverts BLAST or PSI-BLAST output to a multiple alignment byrealigning gapped regions using ClustalW and removing localinconsistencies through comparison with an HMM. HHalign alignstwo alignments with each other by pairwise comparison of HMMsand displays similarities in a profile–profile dotplot.

In the sequence analysis section, we have grouped tools forrepeat identification and analysis of periodic regions in proteins.HHrep is a server for de novo repeat detection that is verysensitive in finding proteins with strongly diverged repeats,such as TIM barrels and ß-propellers (6). REPPER (8)analyzes regions with short gapless repeats in protein sequences.It finds periodicities by Fourier transform and internal sequencesimilarity. The output is complemented by coiled-coil predictionand secondary structure prediction using PSIPRED (18). Aln2Plotshows a graphical overview of average hydrophobicity and sidechain volume in a multiple alignment.

In the secondary structure section, Quick2D integrates the resultsof various secondary structure prediction programs, such asPSIPRED (18), JNET (19) and PROFKing (20), the transmembraneprediction of MEMSAT2 (21) and HMMTOP (22) and the disorderprediction of DISOPRED (23) into a single colored view. TheAlignmentViewer clusters sequences by a sequence idenity criterion,annotates groups of sequences using PSIPRED and MEMSAT2 predictionsof a multiple alignment and graphically displays the resultsin an interactive Java applet.

The tertiary structure section contains Modeller (24) and HHpred(5). Modeller is a very popular program for comparative modeling.It generates a 3D structural model from a sequence alignmentof a protein sequence with one or more structural templates.In contrast to the standalone version of Modeller, the inputformat does not need to be PIR but can also be FASTA or mostother standard multiple alignment formats. Modeller is tightlyintegrated with HHpred, allowing selected hits of HHpred resultsto be used as templates for subsequent comparative modeling.On the results page, models can be evaluated by using a browser-embedded3D-viewer and charts with output from several model qualityassessment programs are provided. This allows fast interactiverefinement cycles of the underlying multiple sequence alignment.The page also provides a link to the iMolTalk server, whichoffers several additional tools for the detailed analysis ofstructures and models (25,26).

In the classification section, we offer modules of the widelyused phylogenetic analysis suite PHYLIP (27), the ANCESCON package(28) for distance bases phylogenetic analysis and CLANS (9).CLANS clusters user-provided sequences based on BLAST pairwisesimilarities (29). The results can be analysed with a CLANSJava applet or can br exported to CLANS format.

Finally, in the utilities section there is a collection of toolswhich help to perform simple tasks that the user will oftenbe confronted with. It includes a sequence reformatting utility,a six-frame translation tool for nucleotide sequences, Extract_gisfor the extraction of gi-numbers from BLAST files, the RetrieveSeqtool for identifier-based sequence retrieval from the non-redundantprotein or nucleotide databases at NCBI, gi2Promotor for theextraction of nucleotide sequences upstream of genes identifiedby the gi-numbers of their encoded proteins and a backtranslationtool.

Future plans

Our own research on protein evolution now heavily depends onthe toolkit server. We will therefore continue to integratenew tools as they become available and improve the usabilityof the toolkit. For instance, a project manager will be addedthat will further facilitate the organization and long-termstorage of job results. On the technical side, we are currentlyin the process of porting the Toolkit to a new Rails-based webframework that permits shorter development cycles and more flexibletool interactions. The new architecture is fully object orientedand renders the Toolkit easily installable. We will packagethe Toolkit framework together with our in-house tools and distributeit freely under the GNU LGPL.

Acknowledgements

We thank Pawel Szczesny for contributing Aln2Plot and TancrdFrickey for many fruitful discussions and developing varioustools. We thank all users who helped to improve our server withtheir questions, feedback, bug reports and tool suggestions.Funding to pay the Open Access publication charges for thisarticle was provided by the Max-Planck society.Conflict of interest statement. None declared.

References

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Table 1

Overview of tools

Tool Source references Description Search     NucleotideBLAST Altschul et al. (11) Sequence search against nucleotide databases (blastn, tblast, tblastx)     ProteinBLAST Altschul et al. (11) Sequence search against protein databases (blastpgp1, blastx)     PSI-BLAST Altschul et al. (12) Iterated sequence search against protein databases     fastHMMER Eddy (13) Fast profile HMM search tool derived from HMMER     HHpred* Söding et al. (5) Sensitive protein homology detection, function and structure prediction by HMM-HMM comparison     HHsenser* Söding et al. (7) Sensitive iterative sequence search based on HMM-HMM comparison     PatternSearch* Unpublished Search for sequences containing a given pattern Alignment     ClustalW Thompson et al. (14) Multiple alignment program for protein and DNA sequences     MUSCLE Edgar (16) Multiple alignment program for protein sequences     ProbCons Do et al. (15) Multiple alignment program for protein sequences     MAFFT Katoh et al. (17) Multiple alignment program for protein and DNA sequences     Blammer* Frickey and Lupas (10) Converts BLAST/PSI-BLAST output to a multiple alignment by realigning gapped regions with Clustal and removing local inconsistencies through comparison to a HMM     HHalign* Söding (30) Comparison of two alignments using HMMs Sequence Analysis     HHrep* Söding et al. (6) Sensitive de novo repeat identification in protein sequences by HMM-HMM comparison     PCOILS* Lupas et al.(31) Coiled-coil prediction     REPPER* Gruber et al. (8) Identification of repeats and their periodicity by Fourier transform and internal sequence comparisons     TPRpred* Unpublished Prediction of TPRs (Tetratrico Peptide Repeats) and related repeats (Pentatrico Peptide Repeats and SEL1-like)     Aln2Plot* Unpublished Graphical overview of average hydrophobicity and side chain volume in a multiple alignment Secondary Structure     Quick2D* Unpublished Concise overview of secondary structure prediction by PSIPRED (18), JNET (19) and PROFKing (20); of coiled-coils by COILS (31); of transmembrane helices by MEMSAT2 (21) and HMMTOP (22) and of natively disordered regions by DISOPRED2 (23)     Alignment Viewer* Unpublished Annotate an alignment with individual PSIPRED (18) and MEMSAT2 (21) predictions Tertiary Structure     Modeller Sali et al. (24) Comparative protein structure modeling by satisfying of spatial restraints     HHpred* Söding et al. (5) Sensitive protein homology detection, function and structure prediction by HMM-HMM comparison Classification     PHYLIP-NEIGHBOR Felsenstein (27) Modules of the phylogenetic analysis package Phylip which allow the construction of distance-based, neighbor-joining trees     CLANS* Frickey and Lupas (9) Clustering tool based on all-against-all BLAST comparisons     ANCESCON Cai et al. (28) Distance-based phylogenetic inference and reconstruction of ancestral protein sequences Utilities     Reformat* Unpublished Sequence reformatting utility     6FrameTranslation* Unpublished Six-frame translation of nucleotide sequences     Extract_gis* Unpublished Extraction of gi-numbers from BLAST files     RetrieveSeq* Unpublished Sequence retrieval from the nr or nt database using a list of identifiers     gi2Promotor* Unpublished Extraction of nucleotide sequences upstream of genes identified by the gi-numbers of their encoded proteins     Backtranslator* Unpublished Reverse translation of amino acids into nucleotide sequences

An asterisk after the toolname indicates that the tool was developed in our group.

A dagger indicates a public tool with extended functionality.

Figure

Figure 1 Input and result pages of PSI-BLAST with overlaid windows for genome databases and Jalview alignment viewer (32). (Click image to enlarge)

 

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