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?
@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:
Get Ensembl Gene IDs for each of your 140 yeast genes.
Go to Ensembl BioMart
Choose the database: 'Ensembl Genes 65'. Then the dataset: 'Saccharomyces cerevisiae genes'
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
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.
Finally, hit the 'Results' button.
If everything looks good. Choose the export options you would like and hit the 'Go' button.
I would still use Ensembl/Biomart for this. Details of this and other approaches can be found in these threads: