Sequence Analysis:

• BIOSCAN : Sequence analysis server. University of North Carolina at Chapel Hill.
• 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 in Israel. Blocks are multiply aligned ungapped segments corresponding to the most hightly conserved regions of proteins.
• CLUSTAL W : Home Page. Multiple Alignment Program. Thompson, J.D.; Higgins, D.G. & Gibson, T.J.
• 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 ). Whashington 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. Hughey, R. & Krogh, A.
• 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 hydorphobicity 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.
  

Ingeborg M.M. van Leeuwen
ingeborg@goliat.ugr.es