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Databases

  • UniProtKB  •  The UniProt Knowledgebase (UniProtKB) 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  •  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

  • Alignment tools  •  Four tools for multiple alignments. [less]
  • BLAST  •  BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs [less]
  • BLAST (UniProt)  •  BLAST sequence similarity search against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB or UniParc - on the UniProt web site. [less]
  • BLAST - NCBI  •  The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.  [less]
  • BLAST - PBIL  •  BLAST search on protein sequence databases [less]
  • Blast2Fasta  •  Converts BLAST output from NCBI to FASTA format. [less]
  • boxshade  •  Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.  [less]
  • ClustalO (UniProt)  •  Align two or more protein sequences on the UniProt web site using ClustalOmega. [less]
  • ClustalW  •  Multiple alignment of nucleic acid and protein sequences. [less]
  • ClustalW - PBIL  •  ClustalW is a general purpose multiple sequence alignment program for DNA or proteins [less]
  • ClustalW2  •  ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. [less]
  • Decrease redundancy  •  Redundancy reduction in a set of aligned or unaligned sequences [less]
  • DIALIGN  •  While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. [less]
  • Dotlet  •  Diagonal plots to graphically compare of biological sequences and identify regions of close similarity [less]
  • FASTA/SSEARCH/GGSEARCH/GLSEARCH  •  This tool provides sequence similarity searching against protein databases using the FASTA suite of programs. FASTA provides a heuristic search with a protein query. FASTX and FASTY translate a DNA query. Optimal searches are available with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).  [less]
  • GENIO/logo  •  Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors [less]
  • Kalign - EBI  •  Kalign is a fast and accurate multiple sequence alignment algorithm. [less]
  • Kalign - SBC  •  Kalign is a fast and accurate multiple sequence alignment algorithm.  [less]
  • LALIGN  •  LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally. [less]
  • MAFFT - CBRC  •  MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. [less]
  • MAFFT - EBI  •  MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. [less]
  • MaxAlign  •  The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. MaxAlign maximizes the number of characters that are present in gap-free columns. It can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.  [less]
  • Multialin  •  Multiple sequence alignment with hierarchical clustering [less]
  • MUSCLE  •  Multiple alignment server [less]
  • 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]
  • pftools  •  The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model. [less]
  • PLOGO  •  Protein sequence logos using relative entropy. [less]
  • PROPSEARCH  •  PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated. [less]
  • Protein Sequence Logos  •  Protein sequence alignment viewed as sequence logos. The total height of the sequence information part is computed as the relative entropy between the observed fractions of a given symbol and the respective a priori probabilities. [less]
  • PVS - Protein Variability Server  •  This server calculates the protein sequence variability within a multiple sequence alignment using several variability metrics. Subsequently, the server can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure.  [less]
  • SAMBA  •  SAMBA is a 128 processor array for speeding up the comparison of biological sequences. The hardware implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty. [less]
  • Seq2Logo  •  Seq2Logo is a web-based sequence logo method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.  [less]
  • SeqLogos  •  SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualize sequence patterns and represent a more informative alternative to consensus sequence [less]
  • Sequence Variability Server  •  This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function. [less]
  • Sequerome  •  Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. [less]
  • 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  •  A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB. [less]
  • T-Coffee - EBI  •  T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.  [less]
  • T-Coffee - WUR  •  T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods. [less]
  • WebLogo  •  Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.  [less]
  • WU BLAST  •  Protein databases query to find regions of sequence similarity quickly, with minimum loss of sensitivity.  [less]