Nucleotide sequences retrieving

Sequences of the genes/cDNAs can be retrieved from databases on the Internet at various web sites. For example, GeneBank (at the National Center for Biotechnology Information, NCBI) is at http //www.ncbi.nlm.nih.gov/ Web/Search/index.html. The EMBL Nucleotide Sequence database (through the European Bioinformatic Institute, EBI) can be found at http //www.ebi.ac.uk/queries/queries.html, whilst that of the DNA Data Bank of Japan is at http //www.ddbj.nig.ac.jp/. 

Entrez (http //www.ncbi.nih.gov/entrez), information retrieval system, integrating NCBI databases of protein and nucleotide sequences, genomes, macromolecular stmctures, and MEDLINE literature database. 

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

As shown in Fig. 1.1, bioinformatics approaches in pharmacogenomics are conducted systematically. The lowest level in the system is at the molecular level. At this level, it is necessary to understand the detailed features of a gene and the relationship between genetic structure and function (see Subheading 1.2.1). These detailed features include sequence analytic information such as sequence retrieval and comparison, sequence variation information such as about single-nucleotide polymorphisms (SNPs), and sequence patterns that can correlate sequence structure to functional motifs. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

The nucleotide sequences can be retrieved from one of the three IC (International Collaboration) nucleotide sequence repositories/databases GenBank, EMBL Nucleotide Sequence Database, and DNA Data Bank of Japan (DDBJ). The retrieval can be conducted via accession numbers or keywords. Keynet (http // www.ba.cnr.it/keynet.html) is a tree browsing database of keywords extracted from... 

Retrieve nucleotide sequences (in fasta format) and restriction maps for one each of bacterial plasmid, cosmid and shuttle vector. 

Retrieve nucleotide sequence encoding mRNA of human (Homo sapiens) soluble aldehdyde dehdrogenase 1 (ALDH1 gil 1429705) and perform gene identification with GeneFinder. 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

Retrieve the nucleotide sequences encoding type C lysozyme precursors from eight organisms and draw their phylogenies of the consensus tree after performing compatibility analysis at WebPhilip. 

Retrieve nucleotide sequences (fasta files) of yeast cytosolic and mitochondrial Gly-tRNA and submit them to RNA folding to obtain their secondary (cloverleal) structures and thermochemical data of foldings. 

Retrieve nucleotide sequence (fasta file) and atomic coordinates (pdb file) of yeast Asp-tRNA. Perform folding analysis/molecular modeling to display graphics of the following ... 

The European Bioinformatics Institute (EBI). This site is located at Hinxton Hall, Cambridge, UK. The home of the EMBL Nucleotide Sequence Database data management tools [including publicly accessible version of SRS—the Sequence Retrieval System (7)] protein family databases microarray tools etc. An extensive repository of resources for bioinformatics. 

GeneSeq . Thomson Derwent s biosequence database, provides information on nucleic and amino acid sequences found in the patent literature. It has biosequence indexing for the patents included in the DWPI database beginning with the very first patents to carry protein and nucleotide sequence descriptions. GeneSeq structure searches retrieve records with the sequence, a short abstract directed to that sequence. 

Nucleotide sequences of nucleic acids can be retrieved from GenBank of the National Center for Biotechnology Information (NCBI) of the National Institute of Health (NIH) at http //www.ncbi.nhn.nih.gov/Genbank, European Bioinformatics Institute (EBI)... 

Protein Identification Resource National Biomedical Research Foundation Georgetown University Medical Center 3900 Reservoir Road, N.W., Washington, DC 20007 Contains nucleotide and amino acid sequences not as extensive in nucleotide sequences as EMBL-GenBank good program environment for quick and easy data retrieval... 

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