Phage Phorum

Gene Functions are typically ascribed by their protein similarity to known proteins.  When doing BLASTs of each gene, look for functions of genes that your subject gene hits.  Good matches to known functions can be attributed to your gene.  The operative word would be "good".  Considerations include:

• low e-value match of Protein blast
• protein Blast with not a good e-value, but maps to a protein structure of known function
• hits to domains with function
• synteny -  Is this particular gene positioned whre only a gene of a certain function could be located. 

Gene Functions are better understood today than they were yesterday.  Historically, we have added function in notes only.  Our rationale was that we had very little experimental data for our inferences.  At the time, it seemed like a good idea.  Today, we have far more data than when we made that decision.  We are more confident in functions based on BLAST data, synteny, and protein data.

Sources of gene functions include:

• BLAST data
• Genome Maps (from Hatfull, 2010)
• Phast functions (excel sheet derived from Hatfull, 2010 data)

Gene Functions are to be added in the notes and function section of the DNAMster file.