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tutorials:mali_nov_09 [2012/03/29 15:36]
jon 		tutorials:mali_nov_09 [2015/09/21 15:29] (current)
hafsa [Querying a protein or gene name at Gene3D]
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 ===== Welcome to Gene3D ===== ===== Welcome to Gene3D =====
 +
 //Fusing structural annotation with genomes and functions.// //Fusing structural annotation with genomes and functions.//
 In this guide you can learn a few things about the types of data in Gene3D, how you can retrieve sets of interest, and what tools are built into the website. There are several ways of beginning your investigation, depending on whether you are interested in particular proteins, superfamilies or genomes, so feel free to jump to the section that best describes what you wish to do and start there. In this guide you can learn a few things about the types of data in Gene3D, how you can retrieve sets of interest, and what tools are built into the website. There are several ways of beginning your investigation, depending on whether you are interested in particular proteins, superfamilies or genomes, so feel free to jump to the section that best describes what you wish to do and start there.
 +
 ===== Querying a protein or gene name at Gene3D ===== ===== Querying a protein or gene name at Gene3D =====
  
 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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-Clicking on the 'Get protein' link for the VAV1 protein thats in ensembl  we get a detailed summary view for this protein [http://gene3d.biochem.ucl.ac.uk/protein/sequence-md5/3b6f9f9024015da2af565d5489f71d1a|Direct link to Results]].+Clicking on the 'Get protein' link for the VAV1 protein thats in ensembl  we get a detailed summary view for this protein [[http://gene3d.biochem.ucl.ac.uk/protein/sequence-md5/3b6f9f9024015da2af565d5489f71d1a|Direct link to Results]].
  
 Th first tab has a summary page of annotations for the protein. Th first tab has a summary page of annotations for the protein.
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 ===== The Protein Collection View ===== ===== The Protein Collection View =====
 In the sequence features tab clicking for VAV1 click on the link  'Click here for Proteins with similar CATH arrangements' and this will retrieve other proteins with a similar domain organisation. Also on this page is a summary of GO annotations and associated evidences for all proteins with this domain organisation. You can then retrieve the sequences from the organism of interest for example for homo sapiens.  In the sequence features tab clicking for VAV1 click on the link  'Click here for Proteins with similar CATH arrangements' and this will retrieve other proteins with a similar domain organisation. Also on this page is a summary of GO annotations and associated evidences for all proteins with this domain organisation. You can then retrieve the sequences from the organism of interest for example for homo sapiens. 
-[http://gene3d.biochem.ucl.ac.uk/proteins/mda/1.10.418.10-1.20.900.10-2.30.29.30-3.30.60.20-2.30.30.40-3.30.505.10-2.30.30.40/taxon/9606|Direct link to Results]].+[[http://gene3d.biochem.ucl.ac.uk/proteins/mda/1.10.418.10-1.20.900.10-2.30.29.30-3.30.60.20-2.30.30.40-3.30.505.10-2.30.30.40/taxon/9606|Direct link to Results]].
 This displays a protein collection page of multiple proteins, further annotation can be obtained from the drop down menu. This displays a protein collection page of multiple proteins, further annotation can be obtained from the drop down menu.
  
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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/superfamily/2.40.128.20|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 find a summary of a genome by searching from the "Get genome summary" tab on the front page. We can find a summary of a genome by searching from the "Get genome summary" tab on the front page.
 For example searching for taxon id 4932 we can see information on superfamilies, funfams, domain organisations etc. of a genome. For example searching for taxon id 4932 we can see information on superfamilies, funfams, domain organisations etc. of a genome.
-[http://gene3d.biochem.ucl.ac.uk/genome/?taxon=4932&db=ensembl|Direct link to Results]]. From each of these pages +[[http://gene3d.biochem.ucl.ac.uk/genome/?taxon=4932&db=ensembl|Direct link to Results]]. From each of these pages 
 its possible to retrieve individual protein sets. its possible to retrieve individual protein sets.
  
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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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