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
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
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.
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
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
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
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
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
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
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
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
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
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
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
etc/options¹ file in the distribution.
This gives you some more on this:
http
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
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
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
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
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
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
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,
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
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
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]
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
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]
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
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
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
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
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
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
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
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
Hi Stefanie
For 3 genomes you need 2 comparison files. In the file requestor window the
more 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,
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]
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
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
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
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]
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
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
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
/
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
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
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
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
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
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)?
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:
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
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
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
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
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
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,
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
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
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
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
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
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
Hi Roy
If you download the latest development version of Artemis (v12.1.1) you can
colour reads for each file differently. So you can then differentiate them
by the file. You can set this colour scheme by right clicking on the BamView
window and selecting 'Colour By'-'Coverage Plot Colours' (the
For ACT, if you want to use shortcuts (other than edit selected feature) on
any of the sequences you need to use the 'ALT' key with the shortcut, e.g.
ALT+T to trim to any met.
Regards
Tim
On 9/16/10 10:09 AM, Oscar Franzén oscar.fran...@ki.se wrote:
Hi!
I'm using ACT to compare three
Hi Jack
Artemis is not really meant as a conversion tool between formats and in
particular EMBL/GenBank to GFF, although it will have a go. You could try
EMBOSS (seqret) to convert. However, it sounds like you have multiple fasta
records in your file which may cause problems if you are writing
PM, Tim Carver t...@sanger.ac.uk wrote:
Hi Kajsa The best way to avoid that is to set up the tracks first. The track
manager works by filtering the features to display and will refresh them when
you click UPDATE. So you should ideally do your editing after you have set
the tracks. Regards On 10
before. Thanks again.
Regards,
-- yealing --
On Fri, Oct 29, 2010 at 4:35 PM, Tim Carver t...@sanger.ac.uk wrote:
Hi Yealing
Thanks for the feedback.
One way to restrict the range on a track is to define it in Artemis first,
i.e. delete the features outside a range by first selecting
Hi Intikhab
Artemis can read in the output from blastall when it is run with the -m 8¹
flag to generate the one line per HSP. It then displays each blast HSP as a
separate feature. The blast needs to be run on the single fasta sequence of
the contigs (rather than a multiple fasta) so that the
Hi Magdalen
Sorry to hear you are having trouble with WebACT. I have tried it a couple
of times and it is working for me. It may be a temporary glitch or possibly
an issue with the size of the sequence. It may be worth trying again?
Regards
Tim
On 2/16/11 3:34 PM, Bossers, Alex
Hi Scott
Yes it is template driven, so there is no -f option. You can manually create
a template or export a template out from a DNAPlotter session. Example
templates can be found in the online manual page:
http://www.sanger.ac.uk/resources/software/dnaplotter/#t_3
The template then restores
Hi Bernd
Thank you for your message. There are command line options for running
Artemis and setting various display parameters, e.g. you can open sequences
and feature tables from different files from the command line. The options
are documented in the user manual. There is no programmer manual
first
view to be the circular plot.
Scott
-Original Message-
From: Tim Carver [mailto:t...@sanger.ac.uk]
Sent: Monday, 21 February 2011 1:32 AM
To: Scott Markel; artemis-users@sanger.ac.uk
Subject: Re: [Artemis-users] launching DnaPlotter with a sequence file
Hi Scott
Yes
Hi Leighton
Actually using .artemis_options in the users home directory works on
windows, or at least on the windows version I have tried it on here.
To find where java thinks the user home directory is there is an application
here:
Hi,
So you constructed the file of genes in Artemis but then you cannot see the
annotation when loaded back in?
One thing to check is that you have not given it a filename with spaces in
the name.
Regards
Tim
On 3/29/11 12:49 PM, Dragica Šalamon salamo...@gmail.com wrote:
Hello, everyone!
Hi Ed
Given a BAM file e.g. x.bam the application is looking for the file
x.bam.bai in the same directory. It sounds this is the case? If you create
the index file with samtools :
samtools index x.bam
then it will create x.bam.bai. You could try re-creating the index with
samtools.
Hi Elena
This may mean that the file is not in the correct format for Artemis to
read. I would recommend you check the Artemis user manual (³Add User Plot²
section) for the supported formats. Alternatively it may be that you just
need to turn scaling on by right clicking on the graph window and
Hi Shahar
You can use the Artemis Navigator under the Goto¹ menu for that. There are
options to find base or amino acid strings.
Regards
Tim
On 6/13/11 12:25 PM, Shahar . shahar...@gmail.com wrote:
Hello,
This is quite basic, but I couldn't figure out how to search for a DNA
sequence or
Hi Florent
Apologies for not getting round to this. It has not been a priority here as
the EMBOSS application 'union' does this. I shall try and promote it up the
todo list.
Regards
Tim
On 8/1/11 7:28 AM, Florent Angly florent.an...@gmail.com wrote:
Hi,
I was trying Artemis to view some
implemented.
Regards
Tim
On 8/1/11 2:47 PM, Tim Carver t...@sanger.ac.uk wrote:
Hi Florent
Apologies for not getting round to this. It has not been a priority here as
the EMBOSS application 'union' does this. I shall try and promote it up the
todo list.
Regards
Tim
On 8/1/11 7:28
Hi Laura
This needs to be configured for your site. You will need the databases to be
searched set up locally and you may need to edit the Artemis scripts that
run blast. There is some documentation in the manual for Configuring the
Run Menu¹.
The error you get may mean that blastall is not in
Hi Feifei
It seems that we can not guarantee the order. Although I did try label and
accession_id on a feature and the order did remain label, accession_id
between saving out to separate files. Were you adding new features or
annotations on features?
Artemis does an auto-save once changes are
Hi Feifei
Artemis is optimised already so that it loads into memory only the reads
that are visible in the display, i.e. for the region you are looking at.
If you have not already done so you should look at increasing the memory
available to Artemis. See below for instructions on how this can be
Hi Zeenia
This is a warning message. Artemis attempts to match the length of the
sequence in the GFF with the sequence lengths in the BAM header. If it
doesn't then it gives that message. It may be worth checking the header of
the BAM.
Regards
Tim
On 2/17/12 4:21 AM, Zeenia Jagga
Hi Qinglu
I suspect these two plots are loaded into Artemis as user plots. So they
probably generated the plot data with scripts and loaded them via the Graph
menu as user plots.
For the strand-specific plot you could generate this via the BAM view by
separating the strands into separate BAM
Hi Louis
You need to read in the bgzip'ed vcf file not the tabix index file. It is
expecting a file to be loaded with the suffix .vcf.gz rather than .tbi. It
will then automatically look for the index (.tbi) file in the same directory
as the VCF file.
Regards
Tim
On 3/17/12 2:48 PM, Louis
Hi Preethi
There is some general JNLP documentation online if you search for jnlp
syntax¹. For Artemis arguments and properties, you may find it useful to
download some of the JNLP files on that webpage and start with those. Below
is one of these examples. The properties and arguments are the
Hi Rudi
One way to achieve this would be to select the features you would like to
add the qualifier to and then from the Edit¹ menu pick Qualifier of
Selected Feature(s)¹ and Change¹. From this window you can add or replace
existing qualifiers and their values, so you can add
?
thanks
Alex
Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk]
namens Tim Carver [t...@sanger.ac.uk]
Verzonden: dinsdag 13 maart 2012 10:23
To: artemis-users@sanger.ac.uk
Onderwerp: [Artemis-users] Artemis and ACT new
=GI:somenumber?
Alex
Van: Bossers, Alex
Verzonden: woensdag 11 april 2012 22:31
To: Tim Carver; artemis-users@sanger.ac.uk
Onderwerp: RE: Artemis and multiple (interactive) annotation tracks
Tim,
thanks for the rapid reply!
I will have a look
postprocess
these files into embl annotation files using the ORF prediction location and
the blast info... Looks lik the dev will exactly show the 4x annotation
feature...hopefully :-)
Will experiment with the hyperlinks
Cheers
Alex
Van: Tim Carver
Hi Sheila
The output of this looks to be a multiple genbank entries in a single file.
Artemis therefore just opens the first contig in the genbank file.
Looking at the example you sent me, you can use EMBOSS to create a multiple
fasta file:
seqret RAST.gbk out.fa
and use union¹ to join the
Hi John
As discussed with you off list but for other users... you can use the output
from blast+ (using outfmt 6) as the comparison file. So you do not actually
need to use the script to generate that.
Regards
Tim
On 10/10/12 2:39 PM, John Legato lega...@nhlbi.nih.gov wrote:
Hello,
We are
Hi Astrid
That message means that one or more of the features in the tab file extends
beyond the end of the sequence. I would check the features in the file and
find which ones are not within the plasmid sequence. Do you have the
additional genes in there as well for example. If you let me know
The new Artemis v15 and ACT v12 are available for download from the website.
Some of the highlights are:
* project file manager, to help group files and make it easier to return to
and open project files (annotation, BAM, VCF).
* SVG (scalable vector graphics) support for producing high
Hi Mike
No there is no way of doing that currently within Artemis (other than
setting the lines to white which you have tried). It may be necessary to
prepare several user plot files with just the data you want to display. I
will look at adding in the option of being able to hide lines from the
Hi Astrid
I would double check that you are working with single FASTA files (not
EMBL/GenBank) when creating the BLAST comparison. Also check that you have
the subject sequence above the query sequence. If not let me know where the
files are and I will take a look.
Regards
Tim
On 13/09/2013
Hi Mircea
I think you have to careful about how you are selecting. If you select the
first CDS in the sequence and then use 'Select'-'Same key' and then use the
Auto Create Gene Names option the numbering will be from left to right. Then
you do the same for 'gene' (using the same start and
In Artemis, with a multi-fasta sequence file, the options for the annotation
file are to use a GFF file or to in some way to concatenate the EMBL/GenBank
feature table (adjusting the coordinates to match the correct position of
the assembly). This is what union¹ should do with EMBL files. I am
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