Question: Homolog Finding
7
gravatar for Plasmid
7.3 years ago by
Plasmid160
European Union
Plasmid160 wrote:

I have a list of 140 yeast proteins and I want to find homolog in human. How can I find both sequence and functional homolog? I tried to use HomoloGene (http://www.ncbi.nlm.nih.gov/homologene). It gave only homologs of some proteins. But I am sure there is other homologs. I also tried to use BLAST but from the blast result it is very difficult to predict homologs when score is low. Is there any database or any tool that can tell the most of yeast proteins homologs in human?

homology protein • 14k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 7.3 years ago by Plasmid160
13
gravatar for Malachi Griffith
7.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

@Alastair lists some very useful threads to help you do this. Using Ensembl BioMart is definitely a quick and easy way to go. For example, you can try the following steps:

  1. Get Ensembl Gene IDs for each of your 140 yeast genes.

  2. Go to Ensembl BioMart

  3. Choose the database: 'Ensembl Genes 65'. Then the dataset: 'Saccharomyces cerevisiae genes'

  4. Hit the 'Filters' button on the left. Then expand the 'Gene' section and check the 'ID list limit' box. Now select the type of IDs from the drop down menu. I'm using Ensembl Gene IDs in the example gene list below but you could use protein IDs or something else. Finally paste your list of IDs into the box. You can try this example ID list (one per line):

    YIL143C YML063W YML092C YPL247C YKR038C YLR354C YBR263W YOR369C

  5. Now hit the 'Attibutes' button on the left. Then select the 'Homologs' option. Now scroll down to the 'Human' section and select the ortholog information you would like to retrieve for each human ortholog of each yeast gene in your list.

  6. Finally, hit the 'Results' button.

  7. If everything looks good. Choose the export options you would like and hit the 'Go' button.


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ADD COMMENTlink written 7.3 years ago by Malachi Griffith17k
4
gravatar for Alastair Kerr
7.3 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

I would still use Ensembl/Biomart for this. Details of this and other approaches can be found in these threads:

ADD COMMENTlink written 7.3 years ago by Alastair Kerr5.2k
1
gravatar for Larry_Parnell
7.3 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

If the BLAST score is low, it can indicate the lack of a homolog. Not every protein must have a homolog in another species, especially a yeast to human.

Use the tools/resources Alastair suggests. +1

ADD COMMENTlink written 7.3 years ago by Larry_Parnell16k
0
gravatar for Manu Prestat
7.3 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

Take a look at Homolens. They use the ensembl homologous db, but the trees are then calculated with phyml, and families can be retrieved by a smart and convenient way using famfetch.

ADD COMMENTlink written 7.3 years ago by Manu Prestat3.9k
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