In this section, we'll be looking at where and how we can retrieve information about genomic features. And this can be gene allocations, promoters, and so on. And the primary two places, I will consider will be the UCSC Table Browser, that comes together with the Geno Browser, and the Ensembi. And that will be demonstrated the first one. So let's go to the UCSC website, genome.ucsc.edu. And while we usually might be using the Genome browser, this time we're going to go to the Table Browser to identify and download the features. So let's see that we would like to download a set of human genes. So we have a number of fields here that we have to fill in. Mammal, we want human. We want to have the latest version of the human genome. So that's December, 2013, hg38. We want the group genes and gene predictions in this query. And Refgenes, as might see there are a number of tracks or a number of data sets that all relate to gene type of information. But were going to stick with refseq. Many of them, most of them are human created sequences. So we can specify the entire genome, but for the purposes of this demonstration, let's just specify a range or rather, a chromosome. Chromosome 22, I'm picking it because it's the shortest one. So it's relatively easy to download. We have a number of filters, we won't be using this at this point. Output format. As you can see, there are a number of output formats we can extract GPF. And we're also going to do it for BD, and then we want the five to be returned to us as plain text. So let's get the output And you can see, we have the genes, and we have the features, exons, coding sequencing. And so on, in the GTA format that we already mentioned. So we can simply go to File > Save As. Save as text, we're going to give it an informative name. So let's say RF Sig, and we're going to say GTF.DAC, and we're going to save the graphic. Now, I'm goona go back and, by just changing this filter, we can we can do BD back. So again, let's get in the output. And we have more information here. We want the whole gene so we're not interested in all the additional features. But, you can evaluate that depending on your particular problem. So push the button to get that data. Sometimes we have to wait. Here's the information in Bed format. Again, you might recognize this as being multi-intervals or multi-axon records with the number of blocks here. And the lengths of each blocks. And then finally, with the relative start position of each block within the ten bank. So it's the same thing, File > Save As. We're going to save it as refSeek, And we're going to specify that it's BD and save. So for the purposes of demonstration, I'm going to show one other type of genomic features namely repeats, arrow repeats in particular. So the genome is the same, human. The version is the same, ng38. Instead of genes and gene predictions, now I'm going to to go to repeats. Keep repeat master here. There are a few other options. Positions, I'm interested in chromosome 22 and it's the full length. And now, there are several classes of repeats, so I'm going to select our repeats because those are the only one's I'm interested in. So repeat name. I'm going to say that match is and I'm going to put the star there for anything else that might come as a suffix. So let's submit this. More information on the filter. We can always edit the filter using this button here. We want it as BED, Browser Expendable Data. In a plain text, just so we can look at it. And get the output. Again, we can ask for context information or just the features themselves. And here they are. All the our repeats and their names. Chromosome, start, end, and so on. And we save this information just like we saved the previous text files. So, I'm going to say that this. So this is how we can download the features from the UCSC payment browser. You can also go to the ensemble website, ensemble.org, and download the entire data sites of our locations. But, we won't be covering that in this presentation. So this concludes the section on how we can retrieve sequences and features.
