I have been working with a bacterial protein of gram negative bacteria. At present, i am in search of its homologs in the closely related and, even in lower eukaryte organisms. So i decided to to perform a genome wide screening to find homologs. As i am very new to bioninformatics, i am in need of directions that could lead me to do screening and to find hidden homologs in the genome. Thank You
Since you are working on bacterial proteins, you would have its sequence information with you. Use ncbi-blast in offine mode with the bacterial protein database.
Do a BLAST search against the genome you want to screen using the sequence of your protein. The top hits will probably be your homolog proteins. BLAST search will simultaneously show the conserved domains present in the query/your protein. Open each sequence and look for the conserved domains using CDD (Show conserved domains option).
If you are working on any particular group of protein or any specific protein than you can use hmmer to find ur homologous sequence.
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