Bioinformatics & Genomics
Protein & Nucleic Acid Search Servers
Fold Recognition Methods
Sequence Database Search Servers
BLAST & Post-Processing
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Aneda, formerly Edinburgh Biocomputing Systems, develops software tools for biologists including the MPSRCH(tm) suite of Smith-Waterman sequence analysis programs which run on general purpose hardware at BLAST-like speeds.
BCM Search Launcher: Nucleic Acid Sequence Searches
[Baylor College of Medicine] Site with multiple tools to search databases for sequences similar to an input query sequence.
BCM Search Launcher: Species-Specific Protein Sequence Searches
[Baylor College of Medicine] A site with multiple tools to search species-specific databases for sequences similar to an input query sequence.
[Weizmann Institute] A server with super-computing power that significantly speeds up a wide variety of homology searches in
sequence databases. Accelerated algorithms include FASTA, BLAST, Smith-Waterman, FrameSearch, Frame+, ProfileSearch, and GeneWise.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
CMS Molecular Biology Resource
[San Diego Supercomputer Center] A compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Moldeling.
[National Center for Biotechnology Information] PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. Using "electronic PCR" (e-PCR), these sites can be detected in DNA sequences, potentially allowing their map locations to be determined.
[EMBL, EBI, Sanger Institute] (Human Genome Server) Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
[IGH Montpellier France] A list of tools including sequence comparison, sequence anotation, and peptide fingerprinting.
[Washington Univ., St. Louis] A protein sequence analysis tool that profiles hidden Markov models (profile HMMs) that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
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[EMBNET] Performs a sequence similarity search against a variety of databases.
[Laboratoire de Minéralogie-Cristallographie] (Patrick Durand) Octopus is an interactive program designed for the rapid interpretation of BLAST, BLAST-2,
and FASTA output text files. It provides an easy-to-use graphical
user interface for both experienced and inexperienced users with
sequence comparison analysis based on the widely-used BLAST series of softwares.
[University College London] A non-redundant composite of the SWISS-PROT, PIR, Genbank (translation), and NRL-3D databases. The OWL server includes a BLAST search and other analysis tools.
The PDB-ISL (PDBintermediate Sequence Library) is a sensitive and fast search procedure. It is useful for finding sequences in the PDB
protein structure database that are homologous to a sequence of unknown structure. PSI-BLAST, Smith Waterman, and FASTA searches are provided.
[EMBL Protein & Peptide Group] A tool for protein database searching by mass spectrometric data, such as peptide mass maps or partial amino acid sequences.
Protein Information Resource
[National Biomedical Research Foundation] (PIR) Collects, organizes, and distributes the International Protein Sequence Database.
[EBI] A local alignment method to search protein sequence databases with a query sequence or multiple alignment, and also allows all pairwise comparisons to be made between a set of sequences and can estimate the statistical significance of the alignments.
Search and Analysis
[DDBJ] A short list of links to common DNA and protein sequence analysis tools.
SWISS-PROT and TrEMBL
[ExPASy] SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy, and high level of integration with other databases. TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT.
[DISC] Performs searches on sequences in protein and DNA databases for similarity to the query sequence, queries can include stop codons and IUPAC ambiguity codes.
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[PBIL] Retrieves sequences allowing a query to be composed from one of the databases available on the server.