Databases

• UniProtKB • functional information on proteins • [more]
  UniProtKB  •  The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium composed of EBI (Rolf Apweiler), PIR (Cathy Wu) and SIB (Swiss-Prot group, Ioannis Xenarios). It is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation). [less]

• MyHits • protein domains database and tools • [more]
  MyHits  •  Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models. [less]

Tools

• BLAST • sequence similarity search • [more]
  BLAST  •  BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs [less]
• boxshade • MSA pretty printer • [more]
  boxshade  •  Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.  [less]
• Decrease redundancy • Sequence redundancy reduction • [more]
  Decrease redundancy  •  Redundancy reduction in a set of aligned or unaligned sequences [less]
• Dotlet • sequence similarity plots • [more]
  Dotlet  •  Diagonal plots to graphically compare of biological sequences and identify regions of close similarity [less]
• MyHits • protein domains database and tools • [more]
  MyHits  •  Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models. [less]
• SIM • binary sequence alignment • [more]
  SIM  •  SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments. [less]
• T-Coffee • sequence and structure multiple alignments • [more]
  T-Coffee  •  A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures [less]