Hi Robert, Are you looing for genes or proteins? As moust genes code proteins it is better to comare proteins.
There are programs what can find orthologs between two organisms. As mutch I understand, you need the list of a proteins what have NOT orthologs in an other genome. So if you find ortolog finder what can give this list as well, you got what you need for protins. The second possibility. Do a megablast one genome against an other genome. Mask 100% identical regions (replace with X). Now remains only regions what are different. Do new blast ( 100% identical sequences are not compared). View the result in ATC. Alternatively use some program/script to check is there (in umnasked region)are genes and what genes. It needs some programming. Regards, Tõnu Margus -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert Minshall Sent: Monday, February 07, 2005 12:47 PM To: [email protected] Subject: [Artemis-users] gene differences Hi all my problem is this. i need to locate gene differences on different strains o bacteria. ACT only shows the similarities NOT differences. diffseq on the emboss platfor wont do what i'm after either. all i want to get is a list of genes found on one genome and not the other a 100% match is not needed although 90% and above would be ideal. Any suggestions at all would be appreciated as my phd is starting to hang on this. Thanks in advance Rob Minshall -- Robert J Minshall Postgraduate Researcher in Microbiology, Biosciences Research Institute, School of Environment and Life Sciences, Lab 209 Cockcroft Building, University of Salford, Salford, Greater Manchester. M5 4WT UK 0161 2952652 [EMAIL PROTECTED] ---------------------------------------------------------------- Concerns about content should be sent to [EMAIL PROTECTED] _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
