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tutorials:mali_nov_09 [2012/08/30 19:25]
admin 		tutorials:mali_nov_09 [2015/09/21 15:29] (current)
hafsa [Querying a protein or gene name at Gene3D]
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 Gene3D can be queried with most recognised identifiers  (e.g. uniprot ID's) along with any gene names provided by these resources. If your query returns more than one sequence, then you will be able to choose the appropriate one from the lists provided. Here we want to find out about VAV1 in human. Enter ‘VAV1’ in the  proteins search type in 'human'  Gene3D can be queried with most recognised identifiers  (e.g. uniprot ID's) along with any gene names provided by these resources. If your query returns more than one sequence, then you will be able to choose the appropriate one from the lists provided. Here we want to find out about VAV1 in human. Enter ‘VAV1’ in the  proteins search type in 'human' 
-in the taxon filter box (to restrict to VAV1 proteins in human) and click 'get proteins' to retrieve the proteins [[http://gene3d.biochem.ucl.ac.uk/proteins/?keywords=VAV1,+&taxon-filter=human|Direct link to Results]].+in the taxon filter box (to restrict to VAV1 proteins in human) and click 'get proteins' to retrieve the proteins [[http://gene3d.biochem.ucl.ac.uk/search?sterm=ABL1&mode=protein|Direct link to Results]].
  
  
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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.
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 ===== Finding Domains in Sequences ===== ===== Finding Domains in Sequences =====
  
-Gene3D also provides [[http://gene3d.biochem.ucl.ac.uk/Gene3DComputeServices/|sequence searching facilities]].  This service also incorporates disordered region prediction and Eukaryotic Linear Motif prediction (ELM).+Gene3D also provides [[http://www.cathdb.info/search/by_fasta|sequence searching facilities]].  This service also incorporates disordered region prediction and Eukaryotic Linear Motif prediction (ELM).
  
 An example sequence is provided by clicking on the 'Example' link. However, VAV_1 provides an interesting case in itself. An example sequence is provided by clicking on the 'Example' link. However, VAV_1 provides an interesting case in itself.
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 Enter this sequence in the search box and hit the green 'Scan Sequence' button. Enter this sequence in the search box and hit the green 'Scan Sequence' button.
  
 +<code>
 MELWRQCTHWLIQCRVLPPSHRVTWDGAQVCELAQALRDGVLLCQLLNNLLPHAINLREVNLRPQMSQFLCLKNIRTFLSTCCEKFGLKRSELFEAFDLFDVQDFGKVIYTLSALSWTPIAQNRGIMPFPTEEESVGDEDIYSGLSDQIDDTVEEDEDLYDCVENEEAEGDEIYEDLMRSEPVSMPPKMTEYDKRCCCLREIQQTEEKYTDTLGSIQQHFLKPLQRFLKPQDIEIIFINIEDLLRVHTHFLKEMKEALGTPGAANLYQVFIKYKERFLVYGRYCSQVESASKHLDRVAAAREDVQMKLEECSQRANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHTQEAMEKENLRLALDAMRDLAQCVNEVKRDNETLRQITNFQLSIENLDQSLAHYGRPKIDGELKITSVERRSKMDRYAFLLDKALLICKRRGDSYDLKDFVNLHSFQVRDDSSGDRDNKKWSHMFLLIEDQGAQGYELFFKTRELKKKWMEQFEMAISNIYPENATANGHDFQMFSFEETTSCKACQMLLRGTFYQGYRCHRCRASAHKECLGRVPPCGRHGQDFPGTMKKDKLHRRAQDKKRNELGLPKMEVFQEYYGLPPPPGAIGPFLRLNPGDIVELTKAEAEQNWWEGRNTSTNEIGWFPCNRVKPYVHGPPQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTTLQFPFKEPEKRTISRPAVGSTKYFGTAKARYDFCARDRSELSLKEGDIIKILNKKGQQGWWRGEIYGRVGWFPANYVEEDYSEYC MELWRQCTHWLIQCRVLPPSHRVTWDGAQVCELAQALRDGVLLCQLLNNLLPHAINLREVNLRPQMSQFLCLKNIRTFLSTCCEKFGLKRSELFEAFDLFDVQDFGKVIYTLSALSWTPIAQNRGIMPFPTEEESVGDEDIYSGLSDQIDDTVEEDEDLYDCVENEEAEGDEIYEDLMRSEPVSMPPKMTEYDKRCCCLREIQQTEEKYTDTLGSIQQHFLKPLQRFLKPQDIEIIFINIEDLLRVHTHFLKEMKEALGTPGAANLYQVFIKYKERFLVYGRYCSQVESASKHLDRVAAAREDVQMKLEECSQRANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHTQEAMEKENLRLALDAMRDLAQCVNEVKRDNETLRQITNFQLSIENLDQSLAHYGRPKIDGELKITSVERRSKMDRYAFLLDKALLICKRRGDSYDLKDFVNLHSFQVRDDSSGDRDNKKWSHMFLLIEDQGAQGYELFFKTRELKKKWMEQFEMAISNIYPENATANGHDFQMFSFEETTSCKACQMLLRGTFYQGYRCHRCRASAHKECLGRVPPCGRHGQDFPGTMKKDKLHRRAQDKKRNELGLPKMEVFQEYYGLPPPPGAIGPFLRLNPGDIVELTKAEAEQNWWEGRNTSTNEIGWFPCNRVKPYVHGPPQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTTLQFPFKEPEKRTISRPAVGSTKYFGTAKARYDFCARDRSELSLKEGDIIKILNKKGQQGWWRGEIYGRVGWFPANYVEEDYSEYC
 +</code>
  
 The main track is the top one, displaying the resolved MDA (the coloured blobs) and all the matches from the various HMM profiles (dotted brackets). Matches from the same superfamily are the same colour, and you can find the E-value by mousing over. Hopefully this image demonstrates two things: (1) The complexity involved in precisely defining domain boundaries (2) The robustness of DomainFinder3 - the in-house algorithm for match selection (paper under review). The main track is the top one, displaying the resolved MDA (the coloured blobs) and all the matches from the various HMM profiles (dotted brackets). Matches from the same superfamily are the same colour, and you can find the E-value by mousing over. Hopefully this image demonstrates two things: (1) The complexity involved in precisely defining domain boundaries (2) The robustness of DomainFinder3 - the in-house algorithm for match selection (paper under review).

Trace:

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