Sequence Analysis

• BLAST: Basic Local Alignment Search Tool. NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases. BLAST 2.0, Psi-BLAST, Phi-BLAST or Ungapped BLAST.
• BLOCKS: Blocks WWW Server. A service for biological sequence analysis at the Weizmann Institute of Science (Israel). Blocks are multiply aligned ungapped segments corresponding to the most hightly conserved regions of proteins.
• CLUSTAL-W: Home Page. Multiple Alignment Program. J.D. Thompson, D.G. Higgins and T.J.Gibson.
• FASTA3: Database search at EBI.
• JALVIEW: A java multiple alignment editor. Release August 1998.
• MAXHOM: MaxHom. Generation of multiple sequence alignments (The PredictProtein server).
• MOTIF: Searching Protein and Nucleic Acid Sequence Motifs. Search several motif libraries (PROSITE, BLOCKS, ProDom, PRINTS,...) for motifs in a query sequence.
• MSA: Form for Multiple Sequence Alignment. Institute for Biomedical Computing (IBC), Washington University.
• PFAM: Protein families database of alignments and HMMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. The Sanger Centre.
• PSA: The Protein Sequence Analysis Server. Prediction of secondary structure and folding classes. Biomolecular Engineering Research Center (BMERC) of Boston University.
• PRINTS: Protein Motif Fingerprint Database. A fingerprint is a group of conserved motifs used to characterise a protein family.
• PRODOM: The Protein Domain Database. The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the Swiss-Prot database. The current version of ProDom was built using an entirely novel procedure based on recursive Psi-BLAST searches.
• PROSITE: A Dictionary of Protein Sites and Patterns. It consists of biological significant sites, patterns and profiles that help to reliable to which known protein family (if any) a new sequence belongs.
• PROTOMAP: (Release 2.0) An automatic hierarchical classification of all Swissprot proteins.
• SAM: Sequence Alignment and Modeling Sofware System. R. Hughey, K. Karplus and A. Krogh. SAM Home Page.
• SAS: Sequences Annoted by Structure. A tool to apply structural information to protein sequences. SAS is a tool which aims to bridge the gap between protein sequence and structural analysis, and aid identification of a protein sequence, by using structural information to recognise distant homologues.
• SOSUI: Clasification and secondary structure prediction of membrane proteins. Based on the physicochemical properties of amino acid sequences such as hydrophobicity and charges. Tokyo University of Agriculture and Technology.
• TMPRED: Prediction of Transmembrane Regions and Orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally ocurring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring.
• WU-BLAST: Home Page. Washington University.
  

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