Sequence annotation

Moszer, I. (1998). The Complete Genome of Bacillus subtilis From Sequence Annotation to Data Arrangement and Analysis. FEBS Lett 430 28. 

Ponting, C. P., Bork, P. (2002). Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242-244. 

This page links the alignments to other sequence-based information. The user will find the coordinates of conserved regions, their sequences, annotations, and other available data. Figure 4 shows the most basic set of options in the Text... 

Letunic, I., L. Goodstadt, N. J. Dickens, T. Doerks, J. Schultz, R. Mott, F. Ciccarelli, R. R. Copley, C. P. Ponting, and R Bork. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 30 242-4. 

Apweiler, R., A. Gateau, S. Contrino, M. J. Martin, V. Junker, C. O Donovan, F. Lang, N. Mitaritonna, S. Kappus, and A. Bairoch. 1997. Protein sequence annotation in the genome era The annotation concept of SWISS-PROT+TREMBL. Proc lnt Conf Intell Syst Mol Biol 5 33M3. 

SeqHound is the basis for many of Blueprint s applications. The BIND Interaction Viewer 3.0 queries SeqHound to recover sequence annotation and interaction information. SeqHound has been used as a back end to replace all previous calls to the NCBI for retrieval of data such as GenBank records, taxonomy traversal, DNA and protein sequence by taxonomy ID or organism, 3D neighbors, and GO traversal. Recently the SeqHound API has been incorporated into Tavema [15], which allows biologists to assemble Web services into a pipeline. The current Web interface allows access only to the sequence aspects of the database, as the primary aim of SeqHound was to be a resource for programmers. However, a more fully featured interface is under development, which will make most of the API s functionality available to nonprogrammers. 

A Seq-aimot is a self-contained package of sequence annotations or information that refers to specific locations on specific Bioseqs. It may contain a feature table, a set of sequence aligmnents, or a set of graphs of attributes along the sequence. 

Figure 4.3. The NCBI Desktop displays a graphical overview of how the record is structured in memory, based on the NCBI data model (see Chapter 2). This view is most useful to a software developer or database sequence annotator. In this example, the submission contains a single Nuc-prot set, which in turn contains a nucleotide and two proteins. Each sequence has features associated with it. BioSource and publication descriptors on the Nuc-prot set apply the same organism Drosophila melanogaster) and the same publication, respectively, to all sequences.

Medigue, C., Rechenmann, F., Danchin, A., and Viari, A. (1999). Imagene an integrated computer environment for sequence annotation and analysis. Bioinformatics. 15, 2-15. 

Sequence annotation is derived from the elastin sequence database (ElastoDB). 

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