GenBank format

Figure 4.2. GenBank format for nucleotide sequence of chicken egg-white lysozyme.

Figure 10.9. Output of GeneView tool of WebGene. The DNA encoding proopiomelanocortin mRNA (1071 bp) is submitted to gene prediction by GeneView at WebGene. The output adapts GenBank format.

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. 

If it is necessary to upload sequence files, these can be compressed using either WinZip, or the UNIX gzip utility, which will significantly reduce the time taken to upload the data. Submitted files should each contain a single sequence in EMBL or FASTA format. It is preferable to use EMBL/Genbank format for uploaded sequences, because any genes annotated in the feature table will then be displayed by ACT. Should multiple sequences be present in an uploaded file, only the first will be used. 

Get GenBank-formatted genome sequences from closely related species and upload these together with the user s sequence into the locally installed dedicated browser system. 

Figure 4.1. Viewing a sequence record with Sequin. The sequence record viewer uses GenBank format, by default. In this example, a CDS feature has been clicked, as indicated by the bar next to its paragraph. Double-clicking on a paragraph will launch an editor for the feature, descriptor, or sequence that was selected. The viewer can be duplicated, and multiple viewers can show the same record in different formats.

This is fundamental to the progress of genomics (and many other areas) of science. Generating data in a common exchangeable format, with a common lexicon of terms [47] in a single non-redundant location is a major goal. A number of examples exist, such as the DNA and protein sequence data in GenBank, EMBL or SwissProt [48-50]. 

There are four textboxes with corresponding data field selectors. After entering querystrings to textboxes and choosing data fields, select sequence formats (embl, fasta or genbank) and then click the Submit Query button to begin the search. 

Pathway Tools can export PGDBs into several different file formats that are described at http //bioinformatics.ai.sri.com/ ptools/flatfile-format.html. These formats include column-delimited tables, SBML (see http //sbml.org/), BioPAX (see http //biopax.org/), Genbank, FASTA, and attribute-value. 

The first databases to appear were DNA sequence databases, namely those from the EMBL (Europe), NCBI (USA) and the DDBJ (Japan), known as EMBL [30], GENBANK [18] and DDBJ [1] respectively. These are DNA databases of sequences and their annotations. These databases continue as a collaborative effort, with the three databases sharing their information. So all three databases contain identical data, albeit in a different format. 

For a more detailed description of FASTA format see www.ncbi.nlm.nih.gov/ BLAST/fasta.html. As an example, the complete set of ORFs from a single species can be found in a format appropriate for ANACONDA in. ffn files of GenBank (ftp //ftp.ncbi.nih.gov/genomes/). If needed, this format must be applied to other sequences before opening them with ANACONDA. 

A Biopipe protocol represents a series of analyses. Each unit of analysis consists of specifications for input, analysis, and output. The input layer consists of a number of adaptors for various common database formats or for remote fetching from Web sources like GenBank. The role of the input layer is to retrieve data into a common format for a subsequent analysis. The complementary output layer contains adaptors to push the analysis result out to the desired database or format. The analysis layer functions through the action of wrapper Biopipe Perl modules that make standard Bioperl runnable binaries accessible to the Biopipe system. An explicit design goal of Biopipe is to reuse the encapsulations of binary tools, importers, and exporters that Bioperl already includes, with thin wrappers that specify the inputs that the input layer must provide in a workflow context. 

ASN. 1 is heavily used at the National Center for Biological Information as a format for exporting GenBank data and can be seen as a means for exchanging binary data with a description of its structure. The access concurrency is like flat files just manageable at file level, there is no support for queries, and it lacks on scalability. But because ASN. 1 files convey the description of its stmc-ture, it thus provides the flexibility that the client side does not necessarily need to know the structure of the data in advance (12). 

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