Sequence retrieval
From MyBio
trocletot pasald chigetcool If you want to carry out sequence-based searches agains sequence databases, you'll probably find the tools in Sequence search more useful. The servers listed on this page is more useful if you know some information other than solely sequence, such as a gene name or accession number, and you want to obtain sequence and other information.
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[edit] Sequence retrieval - Web Resources Descriptions in Detail
NCBI GenBank Search GenBank, PubMed, Entrez, BLAST, OMIM, Books, Taxonomy, or Structure.
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Entrez Gene
includes records from fully sequenced genomes. Data available includes nomenclature, map location, gene products, markers, phenotypes, citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. Data is sourced from both curation and automated integration of data from RefSeq, from collaborating model organism databases and from other databases within NCBI. Records have unique identifiers, in the form of stable and tracked integers. 
Entrez
Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.
SRS Session Start a Permanent Project. Tips Want to know more about using SRS? - go to the Help Center. where you'll find all the searchable online help you need. Where is the old library page? - Click on the 'Library Page' tab on the menu bar. ...
LoadSeq
Using the Efetch parameters allows users to retrieve sequences and analyse them using a plethora of analysis tools.
Recent Hits Acquired from BLAST (ReHAB) is a tool used to find new protein hits in repeated PSI-BLAST searches. ReHAB compares results from PSI-BLAST searches performed with two versions of a protein sequence database and highlights hits that are present only in the updated database. Results are presented in tabular format or in the form of a BLAST-like report, using colors to highlight the new hits. ReHAB is designed to handle large numbers of query sequences, such as whole genomes or sets of genomes. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results; this software greatly simplifies the problem of evaluating the output of large numbers of protein database searches.
BLAST2SRS
Web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases. By allowing the user to control SRS from the BLAST output, BLAST2SRS aims to allow user to restrict output to a subset of homologous genes.
IUBio Biosequences Search and fetch DNA and protein sequences. Text based search and fetch sequences from GenBank, GenBank New, PIR, SwissProt (and updates), TrEMBL (and updates), Prosite (and Prosite doc) specifying search fields such as authors, description, organism, date, keywords or accession.
Public SRS Servers List of sequence retrieval servers open to the general public maintained by Lion Bio.
ORFer Retrieval and management of (large sets of) protein and DNA sequences from NCBI GenBank. ORFer retrieves sets of sequences from GenBank by GI or accession number. For protein sequences, the ORF is generated. Export to Fasta, Excel table or a local database is possible. ORFer an interactive, platform-independent Java program.
SIRW
Web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. eb interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest
The UCSC Table Browser data retrieval tool
Provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database. A flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab- delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks.
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BioRS Sequence retrieval system offering state of the art integration of heterogeneous databanks and other databases with easy-to-use WWW interfaces.. BioRSTM is a powerful and fast retrieval system offering state of the art integration of heterogeneous databanks with other proprietary databases. BioRS enables researches to work with hundreds of biological databases (e.g. sequence, structure, literature) through easy-to-use WWW interfaces. BioRS integrates these heterogeneous pools of information, with different formats and database management systems (DBMS) and allows for multi-field and multi-database queries that normally rely on a unified representation of data. The results generated by a BioRS query may be combined and exported using standardized formats for further analysis.
Entrez Gene Sequence retrieval.
MRS: A fast and compact retrieval system for biological data
Provides tools to rapidly and reliably download, store, index, and query flat-file databanks. Data stored and indexed by MRS takes less space on disk than the raw data, despite that these raw data are included.
MARBL Sequence Retrieval
MARBL: Text Indexing for Genomic Libraries. MARBL is a system to index the text portions of GenBank and associated NLM abstracts. The system is based on Mumps and the MDH. In the following demos, the GenBank files were enhanced with MedLine abstracts.
MartView
Web-based BioMart data retrieval and data mining tool that simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database, facilitating multi-level filtered searches of complex descriptive biological data.
Search GenBank SRS Text-based search of GenBank by specifying fields to search.
