Database GenBank

In the biosciences, a databank (or data bank) is a structured set of raw data, most notably DNA sequences from sequencing projects (e.g. the EMBL and GenBank databases). 

GeneBank (http //www.ncbi.nlm.nih.gov/Genbank/) database directed by the National Center of Biotechnological Information. 

Two hundred and twenty-nine desatl ESTs have been described in Flybase, EMBL or GENBANK databases (May 2003) 221 ESTs have a complete 5 -end, allowing grouping into five different categories of transcripts which only differ in their first exon (Tables 9.1 and 9.2). As shown in Table 9.2, desaturase transcripts have been found with a low abundance in all the tissues tested, except in the head, where they represent a high proportion of the total ESTs (0.2%). The five types of transcripts are not equivalently represented, in particular categories 3 and 5 contain only one EST each. The other three categories of transcripts represent 12 to 73 percent of the ESTs. 

In addition to automated functional annotation of putative 5-HT receptor sequences, determination of open reading frames (ORFs), start codons, and intron/exon boundaries from genomic sequences is now also automated. The absence of expert human curation in such automated annotation can potentially lead to the presence of incorrect sequence data in the databases that has arisen from misidentification of ORFs, start codons, and intron/exon boundaries in raw genomic sequences. For example, the sequences of several chimpanzee 5-HT receptors have recently been added to the GenBank databases, but the sequences given for these receptors indicate that one or several of the seven transmembrane (TM) helices are not present in the sequence, although... 

What are some of the fields that you can use to restrict your search of the GenBank database How many entries did you obtain in your search Explain why you may have obtained several entries in response to your search, as well as what they represent. 

Numerous other putative members of the cupredoxin family can be identified in the GenBank database (http //www.ncbi.nhn.nih.gov). Many of these sequences display remote similarities to other cupredoxins and they therefore cannot be attributed to any of the above described traditional groups. 

Leffers, H., Stetter, K.O. and Garrett, R.A. (1993) EMBL/GenBank databases. Accession Number X72728. 

Kaine, B.P., Schurke, C. and Stetter, K..O. (1991) EMBL/GenBank databases. Accession Number M21087. 

At present, more than 80 complete staphylococcal phage and prophage genomes can be retrieved from the GenBank database, and knowledge about them has opened new possibilities for the understanding of their role in the pathogenicity of the staphylococcal strains (Kwan et al. 2005). 

In hardware sizing and capacity planning, two sources of data are used. The first is the server capacity, often given as a SPEC mark, or the time in which a standard set of procedures is executed. A less-accurate measure of computing capacity is processor speed in cycles per second. Memory size may play a role in some calculations. BLAST queries, for example, are limited by the fetches from the disk the rule is, the more memory the better. Optimally, the entire nonredundant GenBank database can be stored in memory rather than on disk. The second component of the capacity analysis is the computation load, modeled as a typical workload factors. 

Sequence analysis. The GenBank database was searched using the NCBI BLAST program. Consensus sequences were generated and analysed using the programs of the DNASTAR. Multiple alignments of nucleotide were performed with the Clustal... 

EFEa is from E. fetida (GenBank database, AAM73677.1) F-III-1 (BAB40768.1) and F-III-2 (BAB40767.1) are from L. rubellus EFE-B (AAL28118.1) is from L. bimastus. 

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