Re: [Artemis-users] Comparison View Menu, Set Percent ID cutoffs

2005-07-19 Thread Tim Carver
to display. In very coarse terms the higher the % identity the more meaningful that hit may be. As the score comes from using a scoring matrix this cut-off takes into account the similarity as well and so you can also use this when filtering what is being displayed. Best Regards Tim Tim Carver

Re: [Artemis-users] printing gene lists

2005-11-22 Thread Tim Carver
Hi Peter When you get the list of the features, you can right click on the window to get a pop up menu. One of the options on the menu is 'Save List To File'. Regards Tim Tim Carver The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK On 21/11

Re: [Artemis-users] Copy and paste

2005-11-22 Thread Tim Carver
Hi Yung-Yao What you can do is highlight the bases you want by dragging over the feature display with the left hand mouse button held down. The when you have selected the bases you want, go to the 'Write' menu and select 'Bases of Selection' and write them to a file of your chosen format.

Re: [Artemis-users] Cut and paste into dialog boxes

2006-01-04 Thread Tim Carver
Hi Adam I am guessing that you would want to be able to cut and paste the sequence file, from a browser or another application, to open in artemis? This is on the list of things to be implemented so you should see this in the next release. Regards Tim Tim Carver The Wellcome Trust Sanger

Re: [Artemis-users] database

2006-01-26 Thread Tim Carver
Hi Brad Just to let you know that we are currently developing Artemis to be able to talk to a database (CHADO). Currently we have it reading from an internal test database. This is not available yet but will start to become part of the next few Artemis releases as it gets implemented. Regards

Re: [Artemis-users] database

2006-01-26 Thread Tim Carver
Hi Preethi I plan to get a Artemis/ACT release out in the next couple of months (hopefully sooner than later). To get it talking to CHADO it has become more GFF3 compliant which is what we are working towards but this has not been used in anger yet. Regards Tim On 26/1/06 16:18, PIRA (Preethi

Re: [Artemis-users] open several files with several entries at once

2006-06-03 Thread Tim Carver
Hi Marie-Pierre The easiest solution is to make use of the 'art' script and supply the names of the files on the command line: http://www.sanger.ac.uk/Software/Artemis/v8/manual/start.html#RUNNINGUNIX You could then wrap that in a script or define an alias for the command. Regards Tim On

Re: [Artemis-users] problem importing ensembl export view flat files into Artemis

2006-06-22 Thread Tim Carver
Title: Re: [Artemis-users] problem importing ensembl export view flat files into Artemis Hi Lesley Actually I think Artemis doesnt like the location references to another entry, e.g.: FT gene complement(AC012146.25.1.171309:6053..52695) Regards Tim On 22/6/06 17:21, Lesley Nicolson [EMAIL

Re: [Artemis-users] Q1: Configuring run menu

2006-08-29 Thread Tim Carver
/Artemis/v8/manual/ssh-chapter.html Regards Tim Carver On 29/8/06 11:47, Mike Dyall-Smith [EMAIL PROTECTED] wrote: Following on from this thread. Is there a way to query remote databases (Genbank or EMBL) directly using Artemis? I believe there are biopython or bioperl scripts that will do

Re: [Artemis-users] query on Parallelization --- ACT

2006-09-01 Thread Tim Carver
SSH connections. Please let me know if you have other specific questions or want to know more. It may also be good to know where your interests are with ACT. Regards Tim Carver On 1/9/06 12:12, Mangala [EMAIL PROTECTED] wrote: Hi, Plz anyone clarify me the following questions: 1. Is the ACT

Re: [Artemis-users] CHADO connectivity

2006-09-25 Thread Tim Carver
Hi Preethi This is still work in progress. However, I have Artemis reading and writing to a test CHADO database (using either iBatis or straight JDBC) and we have been working on the java interface to do this. This is top priority on my list of things to do over the next few months. If you want

Re: [Artemis-users] Run functional on a Mac?

2006-10-06 Thread Tim Carver
uniprot database You can do this by using the setup_dbs.sh script in Artemis.app/Contents/blast-data cd Artemis.app/Contents/blast-data ./setup_dbs.sh Regards Tim Carver On 5/10/06 19:39, Michael Herron [EMAIL PROTECTED] wrote: Can the items on the Run menu be made to work on an OSX macintosh

Re: [Artemis-users] Preparing Artemis annotation for Sequin submission

2006-10-23 Thread Tim Carver
Title: Re: [Artemis-users] Preparing Artemis annotation for Sequin submission Hi Jay This web service may be of some use to you: http://nbc11.biologie.uni-kl.de/framed/left/menu/auto/right/sequin/index_sequin.shtml ? Regards Tim Carver On 20/10/06 19:48, Jay McCarren [EMAIL PROTECTED

Re: [Artemis-users] ACT v5 for mac - can only see small part of comparison

2006-11-06 Thread Tim Carver
Hi Balasubramanian On 5/11/06 08:23, BALASUBRAMANIAN GANESAN [EMAIL PROTECTED] wrote: Hello I am using ACT v5 for the Mac to look at a two-genome comparison to start off with. Many features seem to not work such as score cutoff, percent ID cutoff are never apllied or saved after setting

RE: [Artemis-users] ACT v5 for mac - can only see small part of comparison

2006-11-06 Thread Tim Carver
Thanks for your suggestions. I will add this to the documentation, possibly as FAQs for ACT. Regards Tim On Mon, 6 Nov 2006, BALASUBRAMANIAN GANESAN wrote: Julian thanks for your suggestions. My comparison looks fine now. I could not find this anywhere on the manual for ACT. May be I did a

[Artemis-users] Re: Can ACT do a protein comparison?

2006-11-07 Thread Tim Carver
Hi Bala No, this is only for DNA sequence comparisons. Regards Tim On 7/11/06 12:02, BALASUBRAMANIAN GANESAN [EMAIL PROTECTED] wrote: Dear Tim/Julian/users Is it also possible to use protein sequence comparisons using this same approach? Regards BALA. = Original Message From Julian

Re: [Artemis-users] Re: Can ACT do a protein comparison?

2006-11-07 Thread Tim Carver
I should add that you can of course use tBLASTx to generate the comarison data. Regards Tim On 7/11/06 13:41, Tim Carver [EMAIL PROTECTED] wrote: Hi Bala No, this is only for DNA sequence comparisons. Regards Tim On 7/11/06 12:02, BALASUBRAMANIAN GANESAN [EMAIL PROTECTED] wrote

Re: [Artemis-users] Re: Can ACT do a protein comparison?

2006-11-08 Thread Tim Carver
blastall -d Seq1_fasta -i Seq2_fasta -p blastn -m 8 -o $outputfile where the input files $sequence_1 $sequence_2 are genbank file or genbank/embl generated by artemis Regards Peter At 2:04 PM + 7/11/06, Tim Carver wrote: I should add that you can of course use tBLASTx to generate the comarison

Re: [Artemis-users] database entry connection failed (mysql problem)

2006-12-04 Thread Tim Carver
Hi Andrew Yes, Artemis will be supporting chado. It will not be limited to postgres but will be using a chado schema. There are currently no plans to support a Bio::DB::GFF database. Regards Tim On 1/12/06 21:50, Andrew Stewart [EMAIL PROTECTED] wrote: I open Artemis Release 8, then proceed

Re: [Artemis-users] color tag

2006-12-06 Thread Tim Carver
Hi Andrew The colours and the default colours for features are defined in the Œetc/options¹ file in the distribution. This gives you some more on this: http://www.sanger.ac.uk/Software/Artemis/v8/manual/concepts.html#CONCEPTS-CO LOUR Regards Tim On 5/12/06 22:47, Andrew Stewart [EMAIL

Re: [Artemis-users] How to print artemis view to paper, not just screenshot?

2006-12-06 Thread Tim Carver
Hi Michael No you cannot really do that with Artemis. You may want to look at the showseq application in EMBOSS which I think will give you what you are looking for in a printable format. Regards Tim On 6/12/06 09:41, Michael Nuhn [EMAIL PROTECTED] wrote: Re: [Artemis-users] color tagHello!

Re: [Artemis-users] color tag

2006-12-06 Thread Tim Carver
file of, say, a unix distribution of Artemis? Thanks, Andrew On Dec 6, 2006, at 3:09 AM, Tim Carver wrote: Hi Andrew The colours and the default colours for features are defined in the Œetc/options¹ file in the distribution. This gives you some more on this: http

Re: [Artemis-users] Import ORFS

2007-01-24 Thread Tim Carver
Hi You can write out the ORFs from Artemis. If you select all the ORF's by going to the Select menu : Select - By key Then create a multiple fasta file by going to Write - Bases of Selection - FASTA format Regards Tim On 24/1/07 15:17, Mekhala Acharya [EMAIL PROTECTED] wrote: Hi, I

Re: [Artemis-users] artemis on ubuntu

2007-01-30 Thread Tim Carver
Hi Stefano I think you can probably just copy 'etc/run_blastp' from version 7 to version 8 then. Regards Tim On 30/1/07 16:16, Stefano Ghignone [EMAIL PROTECTED] wrote: Dear all, ok...I need an help! I have an artemis v.7 working on a FedoraCore3 machine, perfectly integrated

Re: [Artemis-users] artemis on ubuntu

2007-01-30 Thread Tim Carver
is that the script doesn't find the database swissprot! ...even if I create a DATABASE environment variable with the same value as BLASTDB... Any other idea? Stefano Tim Carver wrote: Hi Stefano I think you can probably just copy 'etc/run_blastp' from version 7 to version 8

Re: [Artemis-users] problems with large sequences

2007-04-05 Thread Tim Carver
Hi Nydia You are right it does look like Double ACT has either moved or no longer exists. For WebACT, the best thing to do is to use their 'Contact Us' link to report the problem. Regards Tim On 4/4/07 16:16, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I've been trying to run a

Re: [Artemis-users] Artemis Plugin

2007-04-23 Thread Tim Carver
would suggest you start by getting the code downloaded from CVS. If you want further pointers from then let me know and it would be useful to know more about what you plan. Regards Tim Carver On 23/4/07 17:57, Oliver Krieg [EMAIL PROTECTED] wrote: Hi, I wan't to extend the functionality

Re: [Artemis-users] Fw: [Sanger #29341] SANGER website feedback

2007-04-27 Thread Tim Carver
Hi Andrea What you get in the FASTA header are: systematic name Label Product (if any) Location You should be able to alter what it takes as the first 2 (systematic name and label) in version 9 of Artemis by going to File - Preferences and changing the defaults for Feature Display Labels and

Re: [Artemis-users] Compile Artemis V9

2007-05-01 Thread Tim Carver
Hi Oliver The best thing to do is get the CVS version as described on the Artemis home page (under the Development section). This contains a Makefile and a build.xml file. So you can compile using make: e.g. make clean make Or use the build.xml there to compile with ant. Regards Tim On Tue,

Re: [Artemis-users] short_name?

2007-05-09 Thread Tim Carver
Hi Michael On Tue, 8 May 2007, Michael Herron wrote: On a mac I would like to set the min and max window for a User Plot as described in the Options For Plots and Graphs section. What is the short name for a User Plot? Ther is no short name. Bigger question is can I set options at all on

Re: [Artemis-users] Question / Feature request: ORFs that do not run over contig borders

2007-06-25 Thread Tim Carver
Hi Jack, Scott, This does look to be the best solution at the moment and appears that may have been a quick solution here in the past. I will look at implementing this for the next release. This may take the form of an extra check box on the ³minimum open reading frame² window, so that Artemis

Re: [Artemis-users] changing the orientation

2007-07-02 Thread Tim Carver
Hi Jane Have a look at: http://www.sanger.ac.uk/Software/Artemis/v9/manual/editmenu.html#EDITMENU-RE VERSE-AND-COMPLEMENT-CONTIG This allows contigs to be reverse complemented and there is also the option of contig re-ordering. Regards Tim On 30/6/07 22:02, Christiane Nerz [EMAIL PROTECTED]

Re: [Artemis-users] out-of-range error in ACT

2007-07-26 Thread Tim Carver
Hi Derek I haven't heard reports of this. I *think* DoubleACT may just be expecting fasta format. A quick solution to this is to use the WebACT version and right click in the middle over the comparison part of the window. This should give you a popup menu with an option to save out the comparison

Re: [Artemis-users] Loading mRNA sequence in GenBank format from Entrez Gene

2007-08-07 Thread Tim Carver
Hi Rupert You are right it looks like PRIMARY is a new keyword in RefSeq. I have added this to the code and the changes have been committed. I have also updated the development version that can be found on the Artemis home page. Regards Tim On 6/8/07 22:17, Rupert Millard [EMAIL PROTECTED]

Re: [Artemis-users] Artemis and Java WebStart

2007-08-08 Thread Tim Carver
Hi Michael You probably just need to add '+' to the second argument. This should then reproduce how it is run on the command line, i.e.: art URL1 + URL2 Regards Tim On 8/8/07 14:06, Michael Nuhn [EMAIL PROTECTED] wrote: Hi! I am trying to let our users start Artemis with Java WebStart. I

Re: [Artemis-users] Intergenic region extraction

2007-12-12 Thread Tim Carver
Hi Mel You can use the ŒCreate 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

Re: [Artemis-users] Intergenic region extraction

2007-12-12 Thread Tim Carver
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 ŒCreate Intron Features¹ option under the Create menu

Re: [Artemis-users] Intergenic region extraction

2007-12-13 Thread Tim Carver
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

Re: [Artemis-users] Artemis display issues

2008-02-01 Thread Tim Carver
Hi Filipe It sounds like you are better off using the Frame Line Features... option. This allows you to define what features you want displayed on the frame lines. I think the other option is there for convenience and for when it is suitable. In the development version of Artemis you can have

Re: [Artemis-users] Artemis display issues

2008-02-04 Thread Tim Carver
until the first SPACE (the standard behaviour). That way it is possible to add some description. thanks in adv, FG Tim Carver wrote: Hi Filipe It sounds like you are better off using the Frame Line Features... option. This allows you to define what features you want displayed

Re: [Artemis-users] v9

2008-02-20 Thread Tim Carver
flavour of UNIX are you using and what version of Java? You could try getting the latest Java if you haven¹t already. Regards Tim Carver On 20/2/08 08:57, Duffield Melanie L [EMAIL PROTECTED] wrote: Hi, I am trying to get Artemis v9 set up on a networked Unix computer (or at least co

Re: [Artemis-users] multiple contig reading problem

2008-03-20 Thread Tim Carver
Hi Chris You need to use something like the EMBOSS application 'union'. Separate them into individual EMBL files and concatenate them into a single EMBL entry file (use the -feature option and -sformat embl). Regards Tim On 20/3/08 15:18, Chris Knight [EMAIL PROTECTED] wrote: I am having

Re: [Artemis-users] ACT and more than two genomes

2008-06-23 Thread Tim Carver
Hi Stefanie For 3 genomes you need 2 comparison files. In the file requestor window the Œmore files...¹ button expands the window to allow more sequence and comparison files to be given as input: http://www.sanger.ac.uk/Software/ACT/v7/manual/launch-window.html Regards Tim On 23/6/08 08:06,

Re: [Artemis-users] problem with zooming in/out in ACT

2008-07-17 Thread Tim Carver
Hi Marcus It may help for larger sequences/comparisons to increase the memory you allow ACT to use. If you are using the 'act' script to run it the change the MEM line which will look something like this: MEM=-mx500m -ms20m Regards Tim On 17/7/08 12:31, Marcus Claesson [EMAIL PROTECTED]

Re: [Artemis-users] resolution of Print Image Files

2008-09-03 Thread Tim Carver
Hi Derek, I have added File-Print, so that you can create PostScript files now. (I did look at other options to improve dpi but I think this would require extra image I/O libraries.) I have updated the Development version on the Artemis home page to include this. Regards Tim On 25/8/08 09:53,

Re: [Artemis-users] resolution of Print Image Files

2008-09-05 Thread Tim Carver
stage of proof preparation at least! Cheers Derek At 14:57 03/09/2008, Tim Carver wrote: Hi Derek, I have added File-Print, so that you can create PostScript files now. (I did look at other options to improve dpi but I think this would require extra image I/O libraries.) I have

Re: [Artemis-users] fit longest genome to frame

2008-10-04 Thread Tim Carver
Hi Ben To get the longest sequence scaled to the window, you can 'Select'-'All Bases' in that sequence. Then right click on the feature display of that sequence and select 'Zoom to Selection' from the popup menu. Regards Tim On Fri, 3 Oct 2008, Benjamin C. Kirkup wrote: Artemis users; I'm

Re: [Artemis-users] fit longest genome to frame

2008-10-08 Thread Tim Carver
Hi Janosch Thanks for pointing that out. I will get that fixed, so that it appears in the next development version. Regards Tim On 8/10/08 07:19, j. gröning [EMAIL PROTECTED] wrote: Hello, I'm wondering if anyone noticed that if you use the Navigator to look for an amino acid string in

Re: [Artemis-users] Performance problem generating gene names

2008-10-31 Thread Tim Carver
Thanks Keith. This is fixed now in the development version. Tim On 30/10/08 12:55, Keith James [EMAIL PROTECTED] wrote: I'm trying to add gene names using the automatically create gene names function under the edit menu. Here's the process: 1. Select 4550 CDS features using the feature

Re: [Artemis-users] Possible EOL issue with user plots?

2008-11-03 Thread Tim Carver
Hi Nicole This may well be just Artemis running out of memory. It has to read in the entire file and it is likely that it may be running out of memory before it can display the data. I have changed the code so that it will warn you if this happens ­ this will appear in the next release of

Re: [Artemis-users] can artemis lock/checkout a gene from chado

2008-11-04 Thread Tim Carver
Hi Gowtham Artemis in database mode will not lock the gene. However, if two people edit the same gene it will accept the first changes committed back to the database and warn the second annotator when they commit that changes have been made to that gene. Artemis does this by checking the

Re: [Artemis-users] ACT - percentage id

2008-11-04 Thread Tim Carver
Hi Simon ACT uses the output from BLAST. So it is only a local alignment. You probably need to run a global alignment on your sequences to get the overall percentage identity. Regards Tim On 4/11/08 08:42, Simon Baxter [EMAIL PROTECTED] wrote: Hello, I'm comparing two rather divergent

Re: [Artemis-users] opening a gff file - log4j issue

2008-11-19 Thread Tim Carver
Hi Gareth Those are warnings that can be safely ignored. Have you tried increasing the maximum memory it can use? Look for the line beginning 'MEM=' in the art run script. Are there any message written to the terminal window? Regards Tim On 19/11/08 17:11, Gareth Bloomfield [EMAIL PROTECTED]

Re: [Artemis-users] opening a gff file - log4j issue

2008-11-19 Thread Tim Carver
Tim On 19/11/08 17:17, Tim Carver [EMAIL PROTECTED] wrote: Hi Gareth Those are warnings that can be safely ignored. Have you tried increasing the maximum memory it can use? Look for the line beginning 'MEM=' in the art run script. Are there any message written to the terminal window

Re: [Artemis-users] Configure Run window

2008-12-20 Thread Tim Carver
Hi Aparna To be able to run blast you need to download blast and set up and format your databases. You add the database to the Run menu by editing 'etc/options' and you need to edit the associated run_blastp/run_blastn script for your site. (This means that you need to running this on a UNIX

Re: [Artemis-users] j2ssh.properties File on Windows

2009-01-16 Thread Tim Carver
Hi Chris The easiest thing to do is unwrap the jar and replace it with the file in lib/j2ssh/j2ssh.properties. It is used here to tunnel from windows machines and set off BLAST searches. Regards Tim On 1/16/09 3:44 PM, Chris Friedline cfriedl...@vcu.edu wrote: Hello all, We would like to

[Artemis-users] Artemis and ACT new releases

2009-02-23 Thread Tim Carver
/ Some of the more notable changes are described here with links to the documentation: http://www.sanger.ac.uk/Software/Artemis/v11/index.shtml#changes Regards Tim Carver ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk

Re: [Artemis-users] Artemis output and default options

2009-02-23 Thread Tim Carver
Hi Santiago 1) Is it possible to save the textual summary at the bottom of main Artemis edit window as a text file with tab delimited fields? If you right click on the feature list at the bottom then you get a popup menu with the option Save List To File This will save a space delimited

Re: [Artemis-users] Artemis can't read Chado database

2009-02-26 Thread Tim Carver
Hi Björn I have just added some documentation that describes loading in two examples one of these is the one you have used (NC_008783): http://www.sanger.ac.uk/Software/Artemis/v11/chado/dbloading.shtml I did not experience the problem you seem to have with feature types. However I had to

Re: [Artemis-users] multiple fasta sequence files and feature

2009-02-26 Thread Tim Carver
Hi Malcolm I think the normal trick is to create a single fasta from Artemis by File-Write-All Bases-FASTA format. This then gets them on the correct coordinate system for your query. The GFF multiple contig thing is a problem. It only really copes with a single sequence. I haven't loaded GFFs

Re: [Artemis-users] Feature sets using chado database?

2009-03-05 Thread Tim Carver
Hi Björn There are two ways you can show/hide features in Artemis in database mode. The first is by right clicking on the sequence view and selecting Show/hide features... from the popup menu. This displays a window with a list of visible features and a list of hidden features that can be

Re: [Artemis-users] Bug: crash when loading GFF3 containing multiple sequences

2009-03-16 Thread Tim Carver
Hi Torsten Thanks for that. I have fixed that and I hope to get that in the development version in the next few days. However, there is still a problem that has been mentioned before on the list in that Artemis does not yet take into account column 1 in GFF3 (the ID of the landmark used to

Re: [Artemis-users] vector graphic

2009-03-16 Thread Tim Carver
Hi Daniel Under the File menu there is a Print option. From there you should be able to get it to print a postscript file. Regards Tim On 3/16/09 12:21 PM, Daniel Herlemann herle...@mpi-marburg.mpg.de wrote: Is there a possibility to export the screens as vector-graphic (pdf, ps, eps)?

Re: [Artemis-users] Configuring options for blast, etc for v11 on macosx

2009-03-18 Thread Tim Carver
Hi Rob You can find documentation for setting up blast/fasta and the databases in the Readme.txt in the MacOSX distribution. You can then edit the run_blast* scripts in Artemis.app/Contents/artemis/etc and options file if required as per the documentation in the manual:

Re: [Artemis-users] Configuring Blast with webstart Artemis

2009-03-24 Thread Tim Carver
the blastp and run_blastp scripts.. Thanks very much in advance, Gowthaman SBRI On 3/18/09 3:35 AM, Tim Carver t...@sanger.ac.uk wrote: Hi Rob You can find documentation for setting up blast/fasta and the databases in the Readme.txt in the MacOSX distribution. You can then edit

Re: [Artemis-users] Configuring Blast with Mac Art 11

2009-03-24 Thread Tim Carver
complains as following..but does the JOB Error seen: Fatal server error: Server is already active for display 0 If this server is no longer running, remove /tmp/.X0-lock and start again. AbortDDX Quitting Xquartz... On 3/24/09 11:09 AM, Tim Carver t...@sanger.ac.uk wrote: Hi Gowthaman

Re: [Artemis-users] Is there a public chado db?

2009-06-12 Thread Tim Carver
Hi Matthew You can access GeneDB in read-only mode: db.genedb.org:5432/snapshot?genedb_ro You can access it by launching Artemis from: http://www.sanger.ac.uk/Software/Artemis/v11/database/ In the login menu you can change in the 'Available databases' list to 'GeneDB (read-only)'. This does

Re: [Artemis-users] Is there a public chado db?

2009-06-12 Thread Tim Carver
Hi Matthew You can access GeneDB in read-only mode: db.genedb.org:5432/snapshot?genedb_ro You can access it by launching Artemis from: http://www.sanger.ac.uk/Software/Artemis/v11/database/ In the login menu you can change in the 'Available databases' list to 'GeneDB (read-only)'. This does

Re: [Artemis-users] [Gmod-schema] GMOD/Chado/Artemis eukaryote gene models

2009-06-23 Thread Tim Carver
://www.sanger.ac.uk/Software/Artemis/#development -Tim On 6/8/09 12:10 PM, Leighton Pritchard lpr...@scri.ac.uk wrote: Hi Tim, On 08/06/2009 12:00, Tim Carver t...@sanger.ac.uk wrote: There were a couple of reasons why it was decided to store the gene models in that way in the Pathogen database here

Re: [Artemis-users] changing nt scale in ACT

2009-07-08 Thread Tim Carver
Hi Alex No this isn't possible. The scale obviously changes automatically when you zoom in and out (right hand scroll). However, it sounds as if you want to be able to define the interval of the tick marks which currently you cannot do. Regards Tim On 7/8/09 9:58 AM, Bossers, Alex

Re: [Artemis-users] ACT is sluggish...

2009-08-10 Thread Tim Carver
Hi Kenneth To increase the memory on MaxOSX, you edit this file in the ACT application directory: ACT.app/Contents/Info.plist Towards the bottom of this file there is a line that looks like: string-Xmx512m/string This is the memory limit that you can increase. Regards Tim On 8/7/09 10:49

Re: [Artemis-users] ACT is sluggish...

2009-08-10 Thread Tim Carver
improved. But it is still slow. My computer only has 2 Go of ram so I don't suppose I should increase it more than that. Is there anything else I can do to improve upon performance? Thanks again! Best regards, Kenneth On Mon, Aug 10, 2009 at 9:46 AM, Tim Carver t...@sanger.ac.uk wrote

Re: [Artemis-users] invalid genbank file

2009-08-18 Thread Tim Carver
Hi Ying Or use the development version: http://www.sanger.ac.uk/Software/Artemis/#development Which has a fix for that. Regards Tim On 8/18/09 5:27 AM, Scott Beatson s.beat...@uq.edu.au wrote: Hi Ying, I work-around this by removing the header line that starts with DBLINK from the

Re: [Artemis-users] hyperlinks

2009-09-01 Thread Tim Carver
Hi Alex For database type hyperlinks that are picked up in the feature editor you can add them to the Artemis options file: http://www.sanger.ac.uk/Software/Artemis/v11/manual/options-descriptions.htm l#OPTIONS-HYPERLINKS You could add something like this to that: FILE file:///Users/alex/

Re: [Artemis-users] Size of the input files

2009-09-02 Thread Tim Carver
Hi Santiago This sounds like you need to increase the memory that is available. Have a look at the FAQs 3) 4): http://www.sanger.ac.uk/Software/Artemis/faqs.shtml#faqs Regards Tim On 9/2/09 10:59 AM, Santiago Moreno santiago.mor...@upm.es wrote: Hello to everyone, I have been having

Re: [Artemis-users] Trouble connecting to chado db via artemis

2009-10-07 Thread Tim Carver
Hi John Artemis 11 is the recommended version to be using. One way to diagnose this is to open the Artemis log window if you can. This is under the Options menu in the startup window. From this hopefully you will see what queries it is running. It may be not finding your sequence features. To

Re: [Artemis-users] Problem integrating Artemis with Chado

2009-10-22 Thread Tim Carver
Hi Rohit The first error suggests a strange character in your cvterm table in the column is_relationshiptype. There appears to be a charcter (t?) when the mapping is expecting an integer. You should find that and change it to an integer. The second exception looks like it has failed to find

Re: [Artemis-users] Problem integrating Artemis with Chado

2009-10-26 Thread Tim Carver
to modify for the data I loaded in to the database. This data is available in the wiki link that I gave above and is of the organism Yeast. I really appreciate your help. Thanks and Regards, Rohit On Thu, Oct 22, 2009 at 3:11 PM, Tim Carver t...@sanger.ac.uk wrote: Hi Rohit

Re: [Artemis-users] Problem integrating Artemis with Chado

2009-10-30 Thread Tim Carver
and what the problem is and a solution to this as well. I am attaching the gbk files that I am using as well as the gff file. Please let me know if there are any mistakes in these files that is causing this problem. Regards, Rohit On Tue, Oct 27, 2009 at 3:25 PM, Tim Carver t

Re: [Artemis-users] non-standard genetic code

2009-11-23 Thread Tim Carver
Hi Minou In the initial window that opens up there is an Options menu that lists the available genetic codes. Regards Tim On 11/23/09 11:31 AM, Minou Nowrousian minou.nowrous...@rub.de wrote: Hello, is there a way to change the standard genetic code used in Artemis to one of the

Re: [Artemis-users] Command line option to load data file for ACT

2009-12-29 Thread Tim Carver
Hi Gowtham, You can use something like this: act seq1.embl seq1_v_seq2.comparison seq2.embl for an additional comparison: act seq1.embl seq1_v_seq2.comparison seq2.embl \ seq2_v_seq3.comparison seq3.embl so you can keep adding seqeunce and comparisons files. You would need

Re: [Artemis-users] ACT, transfer annotations

2010-01-21 Thread Tim Carver
Hi Kajsa Unfortunately there is no tool in ACT to do this with flat files. With the database version of Artemis and ACT there is a transfer annotation tool: http://www.sanger.ac.uk/Software/Artemis/v11/chado/overview.shtml#TAT that can be used. I suspect what you are looking for is a bulk

Re: [Artemis-users] Viewing next gen sequence reads on artemis

2010-01-27 Thread Tim Carver
Hi Gowtham Have a look at BamView. http://bamview.sourceforge.net/ This is integrated into Artemis and can be found in the Artemis development version (which is available from the above link as well as the Artemis home page) and will be in the next release. Regards Tim On 1/26/10 8:07 PM,

Re: [Artemis-users] Viewing next gen sequence reads on artemis

2010-02-03 Thread Tim Carver
sequence using the latest version of Mosaik software, but I am unclear on the exact Samtools commands that would convert this into a BAM file suitable for Artemis (sorted and indexed). Is there some info on this? Thank you for your help. Regards, Tony Barbet Tim Carver wrote: Hi

Re: [Artemis-users] Artemis-users post from jocelyne....@epfl.ch requires approval

2010-02-17 Thread Tim Carver
Hi Jocelyne If you use the 'Find/Replace Qualifier Text' option under the Edit menu this should hopefully help. Regards Tim From: Lew Jocelyne jocelyne@epfl.ch Date: Tue, 16 Feb 2010 18:35:30 +0100 To: artemis-users@sanger.ac.uk artemis-users@sanger.ac.uk Conversation: search by key in

Re: [Artemis-users] Artemis Export EMBL

2010-03-03 Thread Tim Carver
Hi Stefanie You could open up the EMBL file and select all CDS features. Then from the File menu - Write - Amino Acids of Selected Features to Qualifier. This will add the /translation qualifier to the selected features. You can then save that out. Regards Tim On 3/3/10 1:05 PM, Stefanie Lager

Re: [Artemis-users] Artemis Export EMBL From GFF

2010-03-04 Thread Tim Carver
Hi Torsten, Stefanie, You could open up the EMBL file and select all CDS features. Then from the File menu - Write - Amino Acids of Selected Features to Qualifier. This will add the /translation qualifier to the selected features. You can then save that out. Wow - I learn a new feature of

Re: [Artemis-users] Artemins and GFF features

2010-03-05 Thread Tim Carver
Hi Stephanie They are warnings and can be ignored in this case. These are controlled by etc/qualifier_types_gff and etc/feature_keys_gff I shall add in tmRNA and in feature_keys_gff and locus_tag. Regards Tim On 3/5/10 1:38 PM, Stefanie Lager stefaniela...@gmail.com wrote: Hi, I'm

[Artemis-users] Artemis and ACT release

2010-03-15 Thread Tim Carver
Artemis (v12) and ACT (v9) have now been released and are available for download from: http://www.sanger.ac.uk/resources/software/artemis/ and http://www.sanger.ac.uk/resources/software/act/ Highlights are a new BAM file viewer, (see http://bamview.sourceforge.net which requires java 1.6+). In

Re: [Artemis-users] Memory for artemis

2010-03-17 Thread Tim Carver
column and the plot value in another column? In this case, what about multiple plots in one file? can we get this from the manual? sorry for asking before I check. -- yealing -- On Tue, Mar 16, 2010 at 8:33 PM, Tim Carver t...@sanger.ac.uk wrote: There is no straightforward way

Re: [Artemis-users] Bam files in ACT?

2010-04-21 Thread Tim Carver
Hi Tony I have just added the ability to open BAM files in ACT. This is now available in the development version from: http://www.sanger.ac.uk/resources/software/act/#t_2 Regards Tim On 4/15/10 5:01 PM, Tony Barbet abar...@nersp.nerdc.ufl.edu wrote: Is there a way to view bam alignment

Re: [Artemis-users] User plots defaults

2010-05-17 Thread Tim Carver
Hi Shahar No unfortunately it is not possible to do this via the options file. You need to do it manually. Regards Tim On 5/17/10 11:29 AM, Shahar . shahar...@gmail.com wrote: Hi,   Is it possible to set the defaults for user plots (e.g. window size, plot height) in the options file?  

Re: [Artemis-users] HTML version of Artemis manual?

2010-05-24 Thread Tim Carver
Hi Torsten Thanks for that, it isn't browsable from the new Sanger website unfortunately but you can download the html from here if you want a local copy: ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v12/artemis_manual_ht ml.zip Regards Tim On 5/24/10 1:02 AM, Torsten Seemann

Re: [Artemis-users] User plot legend

2010-05-24 Thread Tim Carver
Hi Simon Unfortunately you can¹t add your own text. The main issue is obviously space which is why they are just numbered at the moment across the top. In the future I can return to this and perhaps allow the user to set the text and position of the legend. Regards Tim On 5/24/10 6:17 AM,

Re: [Artemis-users] Hide forward and reverse frame lines

2010-05-24 Thread Tim Carver
Hi Shahar No there isn¹t an option for this in the options file. If it would be useful I can add the options : show_forward_lines and show_reverse_lines so that these can be controlled from the options file. This would control both the zoomed out and zoomed in feature displays. Regards Tim

Re: [Artemis-users] Hide forward and reverse frame lines

2010-05-24 Thread Tim Carver
, the first thing I usually do is to manually close them. On Mon, May 24, 2010 at 4:23 PM, Tim Carver t...@sanger.ac.uk wrote: Hi Shahar No there isn¹t an option for this in the options file. If it would be useful I can add the options : show_forward_lines and show_reverse_lines

Re: [Artemis-users] Chado connection Note/note case sensitivity

2010-06-02 Thread Tim Carver
Hi Leighton At the moment it show /note and /comment in database mode. I will look at making it use /Note as well. For now you can change it manually by right clicking on the feature list and using the 'Show Selected Qualifiers ...' option to add the Note qualifiers. Regards Tim On 6/2/10 2:39

Re: [Artemis-users] using ACT tool with mummer output

2010-07-11 Thread Tim Carver
is different from users plot format recommended ACT, so I got error message when I upload) 3. if I upload a dot-plot file, can I select a region and get sequences of there? best regards. Sun-young 2010. 6. 28., 오후 4:50, Tim Carver 작성: Hi There are some useful examples on how to parse

Re: [Artemis-users] Searching for a qualifier?

2010-07-20 Thread Tim Carver
Hi Lionel You can use the feature selector to locate the pseudogenes. From the 'Select' menu open the 'Feature Selector'. Select the Key and Qualifier (CDS and pseudo) to search for and click the 'View' button. This will list those features with that qualifier in a separate window. You can use

Re: [Artemis-users] colour qualifier

2010-07-20 Thread Tim Carver
Hi Stephanie There are two sections in the Artemis manual that are worth looking at in connection with this 'Feature Colours' and 'Setting Colours' (chapter 5). So there are 18 default colours but you can add your own. Regards Tim On 7/20/10 10:17 AM, Stefanie Lager stefaniela...@gmail.com

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