Dengue virus sequence database

In general, the two methods should give the same result, but in some cases they do not, for various reasons, as shall be explained below. Here is a list of useful search tags, which we will explain how to use below:. If you go to the NCBI website , and type one of the search queries above in the search box at the top of the page, the results page will tell you how many matching NCBI records were found in each of the NCBI sub-databases. Alternatively, if you know in advance that you want to search a particular sub-database, for example, the NCBI Protein database, when you go to the NCBI website , you can select that sub-database from the drop-down list above the search box, so that you will search that sub-database:.

The hits are all contigs from the schistosome worm Schistosoma mansoni. Therefore, in Nature volume , page , the Schistosoma mansoni genome sequence was published, along with all the DNA sequence contigs that were sequenced for the genome project, and all the predicted proteins for the gene predictions made in the genome sequence. Note: Schistmosoma mansoni is a parasitic worm that is responsible for causing schistosomiasis , which is classified by the WHO as a neglected tropical disease.

It is possible to use the SeqinR R package to retrieve sequences from these databases. An advantage of the ACNUC database is that it brings together data from various different sources, and makes it easy to search, for example, by using the SeqinR R package. Here are some examples using the query function:. The last thing to do once you have completed your search is to close the connection to the ACNUC sub-database that you were searching, by typing:.

Therefore, to carry out the search, we type in R:. The result of the search is now stored in the list variable Dengue1. Once you have retrieved a sequence, you can then print it out. The variable dengueseq is a vector containing the nucleotide sequence. Each element of the vector contains one nucleotide of the sequence. Therefore, we can print out the first 50 nucleotides of the DEN-1 Dengue genome sequence by typing:.

Note that dengueseq[] refers to the elements of the vector dengueseq with indices from These elements contain the first 50 nucleotides of the DEN-1 Dengue virus genome sequence.

As well as retrieving the DNA or RNA or protein sequence itself, SeqinR can also retrieve all the annotations for the sequence, for example, information on when the sequence was sequenced, who sequenced it, what organism is it from, what paper was it described in, what genes were identified in the sequence, and so on.

For example, to view the annotations for the DEN-1 Dengue virus genome sequence, we type:. Therefore, we can print out the first 20 lines of the NCBI record by typing:. On the left of the annotations, you will see that there is a column containing the field name. When you have finished your running your query and getting the corresponding sequences and annotations, close the connection to the ACNUC sub-database:.

We described above how to search for the sequences published in Nature , using the NCBI website. For example, to search for sequences that were published in Nature , we type:. The line above tells R that we want to store the results of the query in an R list variable called naturepaper. To retrieve these first five sequences, and print out the first 10 nucleotide bases of each sequence, we use the getSequence command, typing:. Microbial genomes are generally smaller than eukaryotic genomes Escherichia coli has about 5 million base pair in its genome, while the human genome is about 3 billion base pairs.

Because they are considerably less expensive to sequence, many microbial genome sequencing projects have been completed. The easiest way to do this is to look at the NCBI Genome website, which lists all fully sequenced genomes and gives the accession numbers for the corresponding DNA sequences. Dengue virus nonstructural protein 3 redistributes fatty acid synthase to sites of viral replication and increases cellular fatty acid synthesis Nicholas S.

Heaton et al. Department of Microbiology, University of Chicago Summary: The public health burden imposed by dengue virus has initiated a quest for drug targets, vaccines, and vector control efforts to prevent human transmission.

This study screened host genes necessary for virus replication with an siRNA library targeting pathways involved in: lipid biogenesis, actin polymerization, ER stress, autophagy, phosphatidylinositol signaling, and cellular vesicular trafficking.

The results of the siRNA screen were then confirmed using pharmacological inhibitors. Immunofluorescence data showed that FASN, which is involved in fatty acid synthesis, relocated closer to the nucleus in infected cells. Dengue virus nonstructural protein 3 redistributes fatty acid synthase to sites of viral replication and increases cellular fatty acid synthesis. PMID: This system is provided for authorized users only. Anyone using this system expressly consents to monitoring while using the system.

Improper use of this system may be referred to law enforcement officials. This project is funded by the U.

This is a collaboration between the University of Chicago and J. Craig Venter Institute. Dengue Virus. Transmission: infects humans via a mosquito vector most commonly Aedes aegypti. Phylogeny: 4 distinct virus types identified, each with multiple genotypes.

Epidemiology: 50 million infected each year worldwide, 2. Clinical: causes dengue fever, dengue hemorrhagic fever, and dengue shock syndrome.

Save to Workbench Sign up for a workbench to:. Browse All Search Types. Browse All Tools. ModBase i Search Gene3D i 1. The information is filed in different subsections. Length: Mass Da : 15, It is useful for tracking sequence updates. The algorithm is described in the ISO standard. Full view. These are stable identifiers and should be used to cite UniProtKB entries.

Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary citable accession number'. See complete history.

Do not show this banner again. This is known as the 'taxonomic identifier' or 'taxid'. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first. SMR i.