| what are the main features of a good genome browser? | Software designed to enable a user to access and display sequence data,Provide a visual correlation for different types of information,Organize large amounts of genome sequence data. |
| what are the common features and differences between genome browsers? | Common features:
• Coordinate system is based on the build
• Zoom in and out
• Gene features aligned to genome
Major Differences:
• Each browser has a very different look and feel
• Navigating through the information |
| what are the three main genome browser repositories? | Ensembl,NCBI (Entrez) - BLAST,UCSC - BLAT. they all use the same human genome assembly but their release timing is different between sites. |
| what are some features of the UCSC browser? | (Vertebrates, Deuterostomes, Insects, Nematodes, Yeast),Entry into genome sequence via BLAT,Table Browser,Creation of PDF, access to all the data produced by the project, and the software used to analyze and present it,Site produces and maintains annotation tracks. |
| what dos the annotation track genomic data mean? | known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies etc.. |
| how are aligned annotation tracks computed? what can users do with it? | Annotation tracks are both computed at UCSC from publicly available sequence data and provided by collaborators, but Users can also add their own custom tracks to the browser. |
| what is UCSC outline? | Navigating, Configuring Browser ,Extracting data |
| how is UCSC navigated? | Graphical Interface, that helps you Control graphical display. |
| what can you find when you search for on the UCSC genome browse regarding the Vast amount of genomic data? | Genome location,Gene ID and amino acid sequence, Gene expression across 53 different tissue types, marks can be found here from 7 different cell lines, DNase I hypersensitivity clusters,DNA conservation across 100 vertebrates, Amino acid conservation across different species, Known SNPs as found in dbSNP, Known repetitive or low complexity regions. |
| does UCSC that helps you find other sources ? | yes ,using Cross-link to the other sources and tools |
| what does configuring mean ? | the Ability to collect that data |
| what are the features of the Ensemble data base? | takes genomic sequence assemblies of human, mouse, rat, mosquito. adds annotation and links (automated process).presents all the data on a web site. |
| what does the Ensemble data base contain? | Chromosome summary,Synteny view,SNP Variation. |
| what is the NCBI genome data viewer's page design comprised of? | GDV is comprised of a series of page elements (widgets) that are used for different types of interactions with the browser, such as genome searches, analysis of BLAST results, data uploads, or changing the display. |
| what do widgets do? | The widgets communicate with one another such that an action in one widget causes other widgets on the page to update. |
