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tutorials:impact_oct_09 [2015/09/17 10:37] hafsa [Finding Domains in a PDB record] |
tutorials:impact_oct_09 [2015/09/17 10:48] (current) hafsa [The Genome comparison page] |
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| We can find a summary of a superfamily by searching from the "Get superfamily summary" tab on the front page. | We can find a summary of a superfamily by searching from the "Get superfamily summary" tab on the front page. | ||
| For example searching for 2.40.128.20 we can see information on functions, domain partners, genome distributions etc | For example searching for 2.40.128.20 we can see information on functions, domain partners, genome distributions etc | ||
| - | [[http://gene3d.biochem.ucl.ac.uk/superfamily/2.40.128.20|Direct link to Results]]. | + | [[http://gene3d.biochem.ucl.ac.uk/search?sterm=+2.40.128.20&mode=family|Direct link to Results]]. |
| If we click on the Domain organisation tab we can see different domain combinations and the organisms they are found in. | If we click on the Domain organisation tab we can see different domain combinations and the organisms they are found in. | ||
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| We can compare 2 genomes by searching from the "Compare Genomes" tab on the front page. | We can compare 2 genomes by searching from the "Compare Genomes" tab on the front page. | ||
| For example lets compare the human pathogen plasmodium vivax and the more lethal species plasmodium falciparum. | For example lets compare the human pathogen plasmodium vivax and the more lethal species plasmodium falciparum. | ||
| - | [[http://gene3d.biochem.ucl.ac.uk/genome/comparison?db=ensembl&taxon-1=PLASMODIUM+FALCIPARUM+3D7&taxon-2=PLASMODIUM+VIVAX|Direct link to Results]]. | + | [[http://gene3d.biochem.ucl.ac.uk/compareTaxons?taxon1=PLASMODIUM+VIVAX&taxon2=PLASMODIUM+FALCIPARUM+3D7&mode=genome|Direct link to Results]]. |
| we can click on individual tabs to see superfamilies, funfams and domain organisations compared between the 2 genomes by their counts of proteins between the two species. | we can click on individual tabs to see superfamilies, funfams and domain organisations compared between the 2 genomes by their counts of proteins between the two species. | ||
| For example on the funfams tab we can see that the "Rifin -like domain" is found in several sequences in P.falciparum and is absent from p.vivax. | For example on the funfams tab we can see that the "Rifin -like domain" is found in several sequences in P.falciparum and is absent from p.vivax. | ||
