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        Links to Sequence Analysis Methods

        Protein Primary Sequence Analysis

        • SAPS
          Methods and algorithms for statistical analysis of protein sequences.
          Brendel V, Bucher P, Nourbakhsh I, Blaisdell BE, Karlin S (1992)
          Proc. Natl. Acad. Sci. USA 89: 2002-2006
        • SignalP
          Identification of prokaryotic and eukaryotic signal peptidesand prediction of their cleavage sites.
          Henrik Nielsen, Jacob Engelbrecht,Søren Brunak and Gunnar von Heijne (1997)
          Protein Engineering 10, 1-6
        • COILS
          Predicting Coled Coils from Protein Sequences
          Lupas A, Van Dyke M and Stock J (1991)
          Science 252:1162-1164
        • big-PI
          Prediction of potential GPI-modification sites in proprotein sequences
          Eisenhaber B., Bork P., Eisenhaber F.
          JMB 292 (3), 741-758
        • TopPred2
          Membrane Protein Structure Prediction, Hydrophobicity Analysis and the Positive-inside Rule
          Gunnar von Heijne (1992)
          J. Mol.Biol. 225, 487-494
        • PSORT
          A knowledge base for predicting protein localization sites in eukaryotic cells
          Nakai K and Kanehisa M (1992)
          Genomics 14, 897-911
        • PredictNLS server
          Finding Nuclear localization signals
          Murat Cokol, Rajesh Nair and Burkhard Rost
          EMBO Reports 1: 411-415
        • PESTfind
          Amino Acid Sequences Common to Rapidly Degraded Proteins: The PEST Hypothesis
          Rogers S, Wells R, Rechsteiner M (1986)
          Science 234, 364-368
        • SEG
          Statistics of local complexity in amino acid sequences and sequence databases
          Wootton, J. C. and S. Federhen (1993)
          Computers in Chemistry 17:149-163.
        • DUST
          SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences
          Hancock, J.M. and Armstrong, J.S. (1994)
          Comput. Applic. Biosci., 10, 67-70
        • XNU
          A streamlined random sequencing strategy for finding coding exons
          Claverie J-M (1994)
          Genomics 23:575-581
        • HMMER
          Multiple alignment using hidden Markov models
          Eddy, S. R. (1995)
          Ismb, 3, 114-20
        • PPSEARCH&PROSITE
          The PROSITE database, its status in 1999
          Hofmann K., Bucher P., Falquet L., Bairoch A (1999)
          Nucleic Acids Res. 27:215-219
        • IMPALA search of the L. Aravind signalling DB
          IMPALA: Matching a Protein Sequence Against a Collection of PSI-BLAST-Constructed Position-Specific Score Matrices
          Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999)
          Bioinformatics 15:1000-1011
          Eukaryotic signalling domain homologues in archaea and bacteria - ancient ancestry and horizontal gene transfer.
          Ponting, CP, Aravind L, Schultz, J, Bork, P, Koonin, EV (1999)
          J. Mol. Biol. 289, 729-745
        • SCOP
          SCOP: a structural classification of proteins database for the investigation of sequences and structures
          Murzin AG, Brenner SE, Hubbard T, Chothia C (1995)
          J. Mol. Biol. 247, 536-540
        • PredictProtein server PHD: predicting one-dimensional protein structure by profile based neural networks
          B Rost (1996)
          Meth. in Enzym., 266, 525-539
        • META server
          Comment: all links to the META services (and the respective publications are in: http://www.embl-heidelberg.de/predictprotein/doc/explain_meta.html
        • Predator
          Seventy-five percent accuracy in protein secondary structure prediction
          Frishman D, Argos P
          Proteins. 1997 Mar;27(3):329-35

        Protein Family Database Search Engines

        • Pfam
          The Pfam Protein Families Database
          Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL (2000)
          Nucleic Acids Research 28:263-266
        • SMART
          SMART, a simple modular architecture research tool: Identification of signalling domains
          Schultz J, Milpetz F, Bork P, and Ponting, CP (1998)
          Proc. Natl. Acad. Sci. USA 95, 5857-5864
        • Interpro Conserved Domain Database
        • eMOTIF SEARCH
        • Prints
        • Blocks Searcher
        • ProDom
        • Pir

          DNA Sequence Analysis

        • NCBI SAGE
          SAGEmap: A public gene expression resource.
          Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF (2000)
          Genome Research. Jul;10(7):1051-60
        • Ensembl BLAST Server
          Ensembl gets a Wellcome boost.
          Butler D (2000)
          Nature Jul 27;406(6794):333.
        • Nucleotide Sequence Analysis @ the CGG WEB server
          FGENESH Salamov A.A., Solovyev V.V. (1999), unpublished data.
          Algorithm is trained on CGG data and based on HMM similar with:
          Genescan (Burge, C. and Karlin, S. (J. Mol. Biol. 1997, 268, 78-94.)
          & Genie (Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. (1996), Proc. Conf. on Int. Systems in Mol. Biol. '96, 134-142)
        • TIGR ESTs
          The TIGR gene indices: reconstruction and representation of expressed gene sequences.
          Quackenbush J, Liang F, Holt I, Pertea G, Upton J (2000)
          Nucleic Acids Res. Jan 1;28(1):141-5
        • PBIL
        • BCM multiple alignment


        Author: Maria Novatchkova (novatchkova@imp.ac.at)
        Last modified: Jan 2001