[Beg-bogas] Getting started with BOGAS
Hi, I have just been trying to annotate my first Ectocarpus gene (Esi0009_0001). And of course, I am struggling with the most basic functions: 1) View alignment: when I click on the button, Java web Start gets launched, "Checking for latest version" then I get this message: Java Web start: Download Error Unable to launch AlignView: a Sequence Alignment Viewer. Details: An error occurred while launching/running the application. Title: AlignView: A Sequence Alignment Viewer Vendor: VIB :: Plant Systems Biology :: Thomas Abeel Category: Download Error Unable to load resource: http://bioinformatics.psb.ugent.be/webtools/alignview/alignview-0.6.jar 2) ESTs: EST is incompatible with the predicted model: is there any way to retrieve easily ESTs sequences from the annotation page, in order to check what is wrong with them (or the gene prediction? Should I do it with Artemis (see below)? 3) Artemis: I have tried to install it on my computer (PC with Windows). So far I have downloaded the file artemis.jar. My Java version is 1.5.0_08 When I double-click on it, I get the following message: Java Virtual Machine Launcher : Invalid or corrupt jar file c:\Program files\artemis.jar Can you help? Thanks a lot in advance, Claire Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon@sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-t... +++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++
Hello Claire,
_1) View alignment:_ when I click on the button, Java web Start gets launched, "Checking for latest version" then I get this message:
Java Web start: Download Error Unable to launch AlignView: a Sequence Alignment Viewer.
Details: An error occurred while launching/running the application.
Title: AlignView: A Sequence Alignment Viewer Vendor: VIB :: Plant Systems Biology :: Thomas Abeel Category: Download Error
Unable to load resource: http://bioinformatics.psb.ugent.be/webtools/alignview/alignview-0.6.jar
Which steps should I take to reproduce this error? I have just now tried to view the aligment for Esi0009_0001 and I encountered no problems.
_2) ESTs: _EST is incompatible with the predicted model: is there any way to retrieve easily ESTs sequences from the annotation page, in order to check what is wrong with them (or the gene prediction? Should I do it with Artemis (see below)?
_3) Artemis_: I have tried to install it on my computer (PC with Windows). So far I have downloaded the file artemis.jar. My Java version is 1.5.0_08 When I double-click on it, I get the following message: Java Virtual Machine Launcher : Invalid or corrupt jar file c:\Program files\artemis.jar
Can you help?
You should not download the artemis.jar file. The Artemis version within the BOGAS platform, called Artemini, is modified from the original Artemis program. This is again a Java Webstart Application. To launch Artemini for a locus, you can select 'Modify using Artemini' under the header 'Gene Structure' on the page that shows after you click the 'Modify This record' button. kind regards, Thomas
Dear Claire,
Hello Claire,
_1) View alignment:_ when I click on the button, Java web Start gets launched, "Checking for latest version" then I get this message:
Java Web start: Download Error Unable to launch AlignView: a Sequence Alignment Viewer.
Details: An error occurred while launching/running the application.
Title: AlignView: A Sequence Alignment Viewer Vendor: VIB :: Plant Systems Biology :: Thomas Abeel Category: Download Error
Unable to load resource: http://bioinformatics.psb.ugent.be/webtools/alignview/alignview-0.6.jar
Which steps should I take to reproduce this error? I have just now tried to view the aligment for Esi0009_0001 and I encountered no problems.
_2) ESTs: _EST is incompatible with the predicted model: is there any way to retrieve easily ESTs sequences from the annotation page, in order to check what is wrong with them (or the gene prediction? Should I do it with Artemis (see below)?
If you open a certain locus in artemini you also get the EST information with it (tagged as Blastn_hit, purple colour). An other possibility (if you want the EST sequences itself) would be to do a blast with the CDS from a certain model against the EST database. you can then download the hit sequences by clicking on the 'F' next to each hit name (in the alignment section). best regards, lieven
_3) Artemis_: I have tried to install it on my computer (PC with Windows). So far I have downloaded the file artemis.jar. My Java version is 1.5.0_08 When I double-click on it, I get the following message: Java Virtual Machine Launcher : Invalid or corrupt jar file c:\Program files\artemis.jar
Can you help?
You should not download the artemis.jar file. The Artemis version within the BOGAS platform, called Artemini, is modified from the original Artemis program. This is again a Java Webstart Application. To launch Artemini for a locus, you can select 'Modify using Artemini' under the header 'Gene Structure' on the page that shows after you click the 'Modify This record' button.
kind regards, Thomas _______________________________________________ Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
Hello, I have just started to annotate the Ectocarpus genome, and I have a few comments / suggestions. Please be indulgent if they are stupid, I have just started a few hours ago! 1. PubMed ID: limited to 2 references, could this be expanded to 4 or 5 (especially useful if annotating according to orthologues from other phyla)? 2. Protein homologs: 2.a. How are the proteins ordered? Is the first one the best BLAST hit? 2.b View BLAST: works when the database is NCBI, not when it is Straminopiles (local database?) 3. ESTs: is there a way of knowing from which library (gametophyte, sporophyte, stress...) they come? Cheers, Claire Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon@sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-t... +++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++
Hello Claire, 1) yes, we can do that. 2) a) They are ordered as the best is on top (based on the Evalue score) b) That's correct. that is fixed in the new version which comes online very soon. 3) For the moment this kind of info is not present in the DB, but based on the name of an EST it should be possible to see from which library it's derived. eg. names who fit : LQ..FA are from gametophyte mature; names that fit LQ..GA are from sporophyte stress. I'll see if I can get the complete list. Then I can try to put this info in the comment field of the ESTs. kind regards, lieven Claire Gachon wrote:
Hello,
I have just started to annotate the Ectocarpus genome, and I have a few comments / suggestions. Please be indulgent if they are stupid, I have just started a few hours ago!
1. PubMed ID: limited to 2 references, could this be expanded to 4 or 5 (especially useful if annotating according to orthologues from other phyla)?
2. Protein homologs: 2.a. How are the proteins ordered? Is the first one the best BLAST hit? 2.b View BLAST: works when the database is NCBI, not when it is Straminopiles (local database?)
3. ESTs: is there a way of knowing from which library (gametophyte, sporophyte, stress...) they come?
Cheers, Claire
Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon@sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-t...
+++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA.
The content of this message may contain personal views which are not the views of SAMS unless specifically stated.
Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++ _______________________________________________ Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
-- ============================================================== Lieven Sterck Predoctoral fellow Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================
Hi Claire, To get more information on the ESTs you can use the following table. Important is the beginning of the names: LQ0AAA... => sporophyte immature non-normalised LQ0AAB... => sporophyte immature normalised LQ0ABA... => stress (cloneminer) LQ0ACA... => gametophyte immature LQ0ADA... => gametophyte immature LQ0AEA... => sporophyte mature LQ0AFA... => gametophyte mature LQ0AGA... => stress (SMART) I've also posted this info on the wiki! kind regards, lieven Claire Gachon wrote:
Hello,
I have just started to annotate the Ectocarpus genome, and I have a few comments / suggestions. Please be indulgent if they are stupid, I have just started a few hours ago!
1. PubMed ID: limited to 2 references, could this be expanded to 4 or 5 (especially useful if annotating according to orthologues from other phyla)?
2. Protein homologs: 2.a. How are the proteins ordered? Is the first one the best BLAST hit? 2.b View BLAST: works when the database is NCBI, not when it is Straminopiles (local database?)
3. ESTs: is there a way of knowing from which library (gametophyte, sporophyte, stress...) they come?
Cheers, Claire
Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon@sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-t...
+++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA.
The content of this message may contain personal views which are not the views of SAMS unless specifically stated.
Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++ _______________________________________________ Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
-- ============================================================== Lieven Sterck Predoctoral fellow Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================
participants (4)
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Claire Gachon -
Lieven Sterck -
lieven sterck
-
Thomas Abeel