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The MPI Bioinformatics Toolkit is an interactive web service which offers access …


Home » Biology Articles » Bioinformatics » The MPI Bioinformatics Toolkit for protein sequence analysis » Table 1

Table 1
- The MPI Bioinformatics Toolkit for protein sequence analysis

Overview of tools

Tool Source references Description

Search
    NucleotideBLAST{dagger} Altschul et al. (11) Sequence search against nucleotide databases (blastn, tblast, tblastx)
    ProteinBLAST{dagger} Altschul et al. (11) Sequence search against protein databases (blastpgp1, blastx)
    PSI-BLAST{dagger} Altschul et al. (12) Iterated sequence search against protein databases
    fastHMMER{dagger} 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    PatternSearch* Unpublished Search for sequences containing a given pattern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    TPRpred* Unpublished Prediction of TPRs (Tetratrico Peptide Repeats) and related repeats (Pentatrico Peptide Repeats and SEL1-like)
    Aln2Plot* Unpublished Graphical overview of average hydrophobicity and side chain volume in a multiple alignment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    Quick2D* Unpublished Concise overview of secondary structure prediction by PSIPRED (18), JNET (19) and PROFKing (20); of coiled-coils by COILS (31); of transmembrane helices by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{dagger} 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.


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