[Artemis-users] clusters
Hello, I think I may be a little ambitious here but I have a cluster of genes on one strand that appear to all be involved in lipopolysaccharide synthesis of bacteria. However,on the opposite strand there appears to be other genes also potentially involved in lipopolysaccharide synthesis. Is there any way of telling from the gene sequence, the GC content etc whether these other genes are also involved in LPS biosynthesis and whether it is under the same control of the other genes. Thanks Mel This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail. Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] v9
Hi, I am trying to get Artemis v9 set up on a networked Unix computer (or at least co-ordinate with our IT people to do this). I have it running locally on a stand-alone but we want to make it more widely available. I now have Artemis runnng but still have some problems. Firstly, I get the messages log4j:WARN No appenders could be found for logger (uk.ac.sanger.artemis.ExternalProgram0. log4j:WARN Please initialize the log4j system properly. Due to our firewire, we can not set up the program to access any external sites so is there a way to remove this message? Secondly I am trying to get blast searches to run. We have local databases set up under a directory that runs the local windows version of blast and the blastall is located in the standalone program version. I have edited options and run_blastp to these two address. When I start a Blastp search, the sequence file is written out to the blastp directory and the message 'blastp process received signal: 2 Ok' comes up but there is no .out file and it seems that blastp doesn't actually run. Is there any way to see error messages (ie if it can't find or access the database or blastall). I have checked for typos and access problems and cant see anything obvious. Finally, when I use control V to view selected feature, the dialogue box is put behind the main Artemis window, can I change the default some where to open it at the front. Apologies that there are so many questions but maybe someone out there has seen something like this before and knows the fixes? Thanks in advance Melanie Duffield Team Leader - Advanced DNA and Protein Technologies Dstl Rm 201, Bld 7a Porton Down Wilts SP4 0JQ +44 (0) 1980 614364 This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail. Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Intergenic region extraction
Hello, I would like to extract all the non-coding region of sequence from my bacterial sequence and write this out to a file. Is there any way of doing this in Artemis? I can select all CDS or genes and I've tried toggle selection but this then selects any features not previously selected rather than DNA sequence not included. Thanks mel This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail. Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[artemis-users] ACT comparisons -
Hello, I am trying to do an ACT comparison using big_blast on two constructions of the same partial genome (one with 4 contigs and one with 3 to see where the various pieces have been joined together). I was therefore expecting large blocks of identical sequence showing rearrangement etc. However, I seem to be getting loads of small blocks. I think that of this is due to multiple repeat elements but I was wondering if it was something to do with the window size used by blastn or the block size by big_blast. Does anyone have any suggestions on how to improve the layout? Thanks in advance Melanie Duffield Bioinformatics Biomedical Sciences Porton Down Wilts SP4 0JQ Tel (1)980 614364 Fax (1)980 614307 This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail. Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing.
