Protein & Nucleic Acid Search Servers

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[Univ. of Michigan] (Naohiro Inohara) Analyzes DNA and protein sequences.

[more info][10346]

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Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.

[more info][12520]

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[Bioinformatics Supercomputer] A single site server for protein or DNA using configurable computing. The user can choose from a number of heuristic and dynamic methods.

[more info][10357]

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[National Center for Biotechnology Information] Provides a General search for nucleotide sequences, protein sequences, biomolecule 3D structures, genomes, taxonomy or literature.

[more info][10360]

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The GeneQuiz system provides highly automated analyses of biological sequences and analyses of complete genomes.

[more info][12512]

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[PBIL] A graphical program for visualizing local alignments between two sequences for proteins and nucleic acids.

[more info][11257]

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Molecular Sequence Megaclassification
[Washington Univ., St. Louis] Provides access to a non-redundant molecular sequence collection that can be accessed by domain type of sequence.

[more info][11014]

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[Computational Biochemistry Research Group] Searches the current release of the SwissProt protein database for entries similar to a given target nucleotide sequence.

[more info][10407]

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[Murdoch University] The Online Researchers Bioinformatics Interface Tools project was established to implement an easy to use web based
interface for registered members of the Murdoch Bioinformatics Research
Group (MBRG). The system provides interfaces to the server side programs BLAST, Repeat Masker, and ClustalW; while still providing a framework for many other programs to be added to the interface in
the future. This is a downloaded Java program.

[more info][12406]

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PredictProtein Server
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.

[more info][10509]

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ScanProsite tool
[ExPASy] Allows the user to browse through a number of databases, such as SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ENZYME, CD40Lbase, and SeqAnalRef; as well as other cross-referenced databases (EMBL/GenBank/DDBJ, OMIM, Medline, FlyBase, ProDom, SGD, and SubtiList). It also allows access to many analytical tools for the identification of proteins, the analysis of their sequences, and the prediction of their tertiary structures.

[more info][10486]

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Software Tools
[TIGR] A list of links to very useful molecular biology and bioinformatics-related freeware. The list includes programs for DNA sequencing and sequence analysis, genomic searches, and microarray image processing.

[more info][12051]

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[Medical Research Council Laboratory of Molecular Biology, Cambridge] The purpose of this server is to provide structural (and hence implied functional) assignments to protein sequences at the Structural Classification of Proteins (SCOP)
superfamily level. SCOP provides a classification of all proteins in the Protein Data Bank (PDB). Whole genome assignment results are also provided.

[more info][14065]