|BANCHE DATI BIOLOGICHE|
Analisi di una regione genomica di interesse
1 Mappa fisica (MapView)
The NCBI Site Map summarizes the available human genome resources and provides a brief description of each one. The Human Genome Sequencing web site summarizes sequencing progress for each chromosome and provides access the the sequence data as well as related information. The NCBI Map Viewer provides graphical displays of features on NCBI's assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps. Release notes report changes in MapView displays or modifications in algorithms used to make the assembly and its annotation, with statistics being provided for each build.
Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map; see assembly description), the BAC tiling path (the 'GenBank' map), and the location of genes, STSs, FISH mapped clones, ESTs, GenomeScan models, and variation.
You can find genes or markers of interest by submitting a query against the whole genome, or a chromosome at a time. Results are indicated both graphically, as tick marks on the ideogram, and in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display is that including the Gene_Sequence, GenomeScan, and UniGene maps. You can also browse a chromosome by clicking on a chromosome link in the ideogram.
The Human Genome Sequence
As the Human Genome Project finishes off the sequence of the human genome, NCBI is making a number of resources available to the public to facilitate the widespread use of this valuable resource.
Finished Contigs of Genomic Sequence. NCBI has been producing contigs of finished sequence and assigning them accession numbers beginning with NT_ for some time. These contigs are assembled based on information from the sequencing centers and by examining sequence overlap. NT_ records are shown in the Contig map of the Map Viewer and have been available for ftp in a number of formats.)
Draft Contigs of Genomic Sequence: NCBI has been working on assembling draft sequence into contigs as well. This is a more challenging problem since draft sequence is by definition still not complete. Each clone consists of a number of fragments and the relationships between clones may not be known. Through a process of comparing the sequences to each other and to known mRNAs, ESTs, and BAC end sequences, it is possible to infer a layout of the clones into an ordered series with overlaps. This has been done by NCBI for the submitted draft sequence, and is what is shown in the GenBank map of the Map Viewer. There are some additional steps necessary to infer the detailed sequence itself, which involves ordering and orienting the fragments within the clones. This process is underway, and when complete, the draft sequence contigs will be made available for ftp as well. Until then, the components, as they were submitted to GenBank by the human genome sequencing centers, are available in the hs_phase*.fna.gz files on the ftp site.
Annotation: The contigs are then annotated by comparing them to known mRNAs to place known genes on the sequence. STS markers are placed on the contigs by a method known as electronic PCR. These markers can be compared with the various STS maps shown in the map viewer to place the contigs onto the chromosomes. The STSs can also be used to place annotation on human variation from the dbSNP databases.
Gene Prediction: Finally, new genes can be predicted in between the known genes placed by mRNA alignment. Prediction of new genes is not an exact science and involves a substantial research component combining information on codon frequency, possible splice sites, and the positions of ESTs. This process is also underway at NCBI. Once the draft contigs are established to the sequence level, gene prediction will be done over the whole genome, and the predicted proteins also made available on the NCBI ftp site. Other groups will be making their own predictions, enabling all the public participants to compare their results and learn from each other, with the expectation that we will gradually converge on a commonly accepted set of predictions.
Additional information about the human maps and resources around the known human genes are available from the appropriate sites at NCBI.
Hs Release notes
Uso di Genome Browser per l’annotazione di Gaps della sequenza genomica,
STS, geni noti, Trascritti, ESTs
Human Genome Project Working Draft
This site contains a working draft of the human genome, which is over 90% complete. Approximately half of the sequence is in a highly accurate 'finished' state. The other half is merely 'draft' quality. Some care must be taken interpreting draft regions, but these are still often
very useful to the working scientist. We encourage you to explore the working draft with the genome browser, which displays the work of many annotators worldwide.
Human Genome Server
Ensembl is a joint project (primarily funded by the Wellcome Trust) between EMBL - EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
Page by Stefania Bortoluzzi, October 5, 2001