Jessica Walter
Paramjeet S. Bagga,  Ph.D.

Sequence Retrieval Systems

ACNUC Database Management System
ACNUC is a retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence databases SWISS-PROT or NBRF. The SWISS-PROT database is supplemented with the TrEMBL data in order to obtain a complete protein sequence database.
ATLAS: Atlas Retreival System
ATLAS is a mutlidatabase information retrieval program specifically designed to access macromolecular sequence databases.
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 analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. 
Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences
An interactive tool for peptide and nucleotide sequence analysis. A growing library of functions for sequence management and analysis, statistics, numerics, graphics, parallel execution and more.
DNA-Today 
DBGET is a simple database retrieval system for finding and obtaining specific entries of diverse databases.
ENTREZ
Provides integrated access to biomedical literature, nucleotide and protein sequences, along with 3-D protein structures, complete genomes and population study data sets. Pre-computed similarity searches are available for most database records producing a list of related sequences, structure neighbors, as well as related articles.
ExPASy Molecular Biology Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
ExPASy_SWISS-PROT
Sequence retrieval from SWISS-PROT and TrEMBL. 
ExPASy_TrEMBL
A protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT. 
ExPASy_TrEMBL_NEW
TrEMBL_NEW consists of the translation of all new and updated CDS in EMBL since the last TrEMBL release. It is partially redundant with SWISS-PROT and TrEMBL.
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. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits.
NCBI_GenBank
An annotated collection of all publicly available nucleotide and amino acid sequences.
NCBI_LocusLink
Provides a single query interface to curated sequence and descriptive information about genetic loci, presenting information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and related web sites.
NCBI_RefSeq: Reference Sequence Project
A database of non-redundant reference sequences standards, including genomic DNA contigs, mRNAs and proteins for known genes. These provide a stable reference point for mutation analysis, gene expression studies, and polymorphism discovery.
NUCLPEPSEARCH
Searches Swiss-Prot for a nucleotide sequence.
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
SRS: Sequence Retrieval System
Searches various databanks to retrieve a protein, DNA/RNA sequences, gene maps, mutants, 3D structures, metabolic pathways and much more. 
SRS-FASTA
This is a service to match your query sequence against subsets of nucleic and protein databanks. These subsets are chosen by you with keyword selections in the sequence documentation.
The Genome Channel
A tool for the comprehensive sequence-based view of genomes.
Virtual Genome Center
This website provides several bioinformatics tools ranging from database searches to a variety of sequence analysis tools.
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