Re: [Artemis-users] Intergenic region extraction
For those interested in doing this: I have added an option in Artemis under the Create menu to create features in the intergenic regions. If you want to try this new function it is in the development version. Look for the ³Development² section on the Artemis homepage and click on LAUNCH ARTEMIS or download it from: http://www.sanger.ac.uk/Software/Artemis/v9/v9_9/artemis_v9_9.jar (for windows) Or http://www.sanger.ac.uk/Software/Artemis/v9/v9_9/artemis_compiled_v9_9.tar.g z (for UNIX) -Tim On 12/12/07 09:39, Duffield Melanie L [EMAIL PROTECTED] wrote: 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 The Information contained in this E-Mail and any subsequent correspondence is private and is intended solely for the intended recipient(s). For those other than the recipient any disclosure, copying, distribution, or any action taken or omitted to be taken in reliance on such information is prohibited and may be unlawful. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Intergenic region extraction
Hi Mel You can use the Create Intron Features¹ option under the Create menu and then write those to file. Regards Tim On 12/12/07 09:39, Duffield Melanie L [EMAIL PROTECTED] wrote: 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 The Information contained in this E-Mail and any subsequent correspondence is private and is intended solely for the intended recipient(s). For those other than the recipient any disclosure, copying, distribution, or any action taken or omitted to be taken in reliance on such information is prohibited and may be unlawful. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Intergenic region extraction
Opps. I just realised that isn¹t exactly what you meant. I am not sure that there is a way of doing this in Artemis easily and you may need a script. Tim On 12/12/07 10:40, Tim Carver [EMAIL PROTECTED] wrote: Hi Mel You can use the Create Intron Features¹ option under the Create menu and then write those to file. Regards Tim On 12/12/07 09:39, Duffield Melanie L [EMAIL PROTECTED] wrote: 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 The Information contained in this E-Mail and any subsequent correspondence is private and is intended solely for the intended recipient(s). For those other than the recipient any disclosure, copying, distribution, or any action taken or omitted to be taken in reliance on such information is prohibited and may be unlawful. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
RE: [Artemis-users] Intergenic region extraction
Hi How about using something like EMBOSS - maskfeat on an entry saved in EMBL format http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html best wishes Andrew From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tim Carver Sent: 12 December 2007 10:41 To: Duffield Melanie L; artemis-users@sanger.ac.uk Subject: Re: [Artemis-users] Intergenic region extraction Hi Mel You can use the 'Create Intron Features' option under the Create menu and then write those to file. Regards Tim On 12/12/07 09:39, Duffield Melanie L [EMAIL PROTECTED] wrote: 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 The Information contained in this E-Mail and any subsequent correspondence is private and is intended solely for the intended recipient(s). For those other than the recipient any disclosure, copying, distribution, or any action taken or omitted to be taken in reliance on such information is prohibited and may be unlawful. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users -- Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. This email and any attachments are believed to be free from viruses but BBSRC accepts no liability in connection therewith. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
