A Field Guide to GenBank and NCBI Molecular Biology Resources A lecture and hands-on computer workshop on GenBank and related databases covering effective use of the Entrez text search service and the BLAST similarity search engine.

BCM: Baylor College of Medicine The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches.

BIMAS_WWW Signal Scan Finds and lists homologies of published signal sequences with the input DNA sequence.

BIOLOGY WORKBENCH The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analyses and modeling tools, all within a point and click interface that eliminates file format compatibility problems.

BLASTula Identifies the function of newly discovered genes, characterize new sequences by performing extremely rapid comparisons against various large DNA and/or protein sequence databases.

BLOCKS WWW Server Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively.

DIP: Database for Interacting Proteins This set of Web pages will allow you to: search the DIP database, to submit new protein-protein, and to update database entries by adding new references to the DIP.

ExPASy_AACompIdent Tool A tool which allows the identification of a protein from its amino acid composition. It searches the SWISS-PROT and/or TrEMBL databases for proteins, whose amino acid compositions are closest to the amino acid composition given.

ExPASy_AACompSim Tool A tool which allows the comparison of the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry.

ExPASy_SWISS-PROT Sequence retrieval from SWISS-PROT and TrEMBL.

ExPASy_SWISS-PDB Viewer An application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

GeneQuiz An integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases. It focuses on deriving a predicted protein function, based on the available evidence, including the evaluation of the similarity to the closest homologue in the database (identical, clear, tentative, or marginal).

KEYNET A database of Keywords extracted from EMBL and GenBank databases. The Keynet structure is based on biological criteria aimed to assist the user in data searching and to minimize the risk of loss of information.

NCBI_BLAST: Basic Local Alignment Search Tool A set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.

NCBI_MMDB: Molecular Modeling DataBase MMDB contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from PDB. The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy. MMDB structural data of proteins are compared against each other using the VAST algorithm for detecting significantly similar substructures.

NCBI_PCR 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.

PATSCAN A pattern matcher, which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern, which you input.

PBIL_NPS@ Sequence similarity search with FASTA, BLAST, PSI-BLAST, and SSEARCH on protein databases such as SWISS-PROT, SP-TReMBL or NRL_3D. Sites and signatures detection with PATTINPROT or PROSCAN. Multiple alignment with CLUSTALW or MULTALIN.

PDB3D: realtime 3d molecule renderer for the www A high-speed 3D molecule rendering applet which has been designed specifically for viewing Protein Data Bank (PDB) format molecular structure files within web pages.

PepPepSearch Search Swiss-Prot for a peptide sequence.

Protein Hydrophilicity/Hydrophobicity Search and Comparison Server Provides tools for plotting, comparing and searching a library for similarities, of a protein's hydropathy profile.

Repeatmasker Web Server Repeat Masker screens DNA sequences in Fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.

SRS-FASTA This is a service to match your query sequence against subsets of nucleic and protein databanks. You choose these subsets with keyword selections in the sequence documentation.

THE GENE DISCOVERY PAGE If your sequence analysis needs are basic, you are invited to use The Gene Discovery Page for your Bioinformatics solutions. The Gene Discovery Page organizes select web-accessible bioinformatics tools in a coherent fashion.

THE GENOME CHANNEL A tool for the comprehensive sequence-based view of genomes.

THE MEME SYSTEM Discover motifs in groups of related DNA or protein sequences using MEME and search sequence databases using motifs using MAST.

Virtual Genome Center This website provides several bioinformatics tools ranging from database searches to a variety of sequence analysis tools.

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