November 2012 - beg-bogas@psb.ugent.be

[Beg-bogas] Search for ambiguous aa motifs with GenomeView
by Alexander Schober 19 Jan '13

19 Jan '13

Hi Thomas Abeel, i am a new student at SAMS and have just started to work on a LRR-ROCO project with my supervisor Claire Gachon. We already wrote an email yesterday, and therefore i wanted to thank you for your kind answer! Unfortunately we came up with another little problem regarding the handling of GenomeView. I opened up a random locus (e.g. Esi0003_0092) and tried to search for an ambiguous amino acid motif(e.g. LxxLxLxxNxL), using the Ctrl+F command. Sadly, i was not able to feed in the query motif in a proper way to get hits. (tried: stars, dots, dashes... also considered faq and manual) How do i have to type in the ambiguous amino acids within an motif to get hits? Thank you very much in advance! Best wishes and a nice weekend, Alex

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[Beg-bogas] Could my new student have editing rights in the Ectocarpus genome ?
by Claire Gachon 21 Nov '12

21 Nov '12

Hi Thomas / Lieven, My new student Alexander Schober, is currently working on updating the annotation of the LRR-ROCO and NB-ARC-TPRs in Ectocarpus, based on the new RNAseq data available from Roscoff. There are a few structures that he would like to modify, and I was wondering whether it would be possible for him to have his own login, so that his modifications are easily tractable. Can you let me know if and how we could arrange this? Many thanks in advance, Claire ++++++++++++++++++++++++++++++++++++ Dr Claire GACHON Principal Investigator in Molecular Phycology Scottish Association for Marine Science Scottish Marine Institute PA37 1QA Oban United Kingdom claire.gachon(a)sams.ac.uk Skype contact : claire.gachon Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/claire-gachon <http://www.sams.ac.uk/claire-gachon%0b>+++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS Research Services Ltd a Limited Company (SC224404). All Companies in the group are registered in Scotland and share a registered office at Scottish Marine Institute, 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.

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[Beg-bogas] GenomeView mysteries...
by Claire Gachon 08 Nov '12

08 Nov '12

Hi Lieven, With my new student Alexander Schober, we've become very interested in new tracks that have appeared in Genome View. However, we're not quite sure what we are looking at. Let's take Esi0207_0011 as a (purely random) example. 1) Can you explain to us what the pinkish track (e.g. sctg11.sort.bam) exactly is? Are we correct in thinking these are RNAseq data (single reads, non paired-end?) 2) Same question for "junctions": are these intron-exon borders mapped based on the above RNAseq reads? 3) on the sctg11.sort.bam track, is it significant that some reads (the blue ones) are mapped in reverse orientation, when the gene is obviously on the + strand? 4) if we want to look in detail at one RNAseq read or at a junction (e.g. to check some alternative splicing, funky LRR recombination, or the mismatch at 1125201), can we easily retrieve the correponding sequence from somewhere? Sorry to ask so many questions, but at least this time, I haven't accidentally hacked into BOGAS! Best, Claire ++++++++++++++++++++++++++++++++++++ Dr Claire GACHON Principal Investigator in Molecular Phycology Scottish Association for Marine Science Scottish Marine Institute PA37 1QA Oban United Kingdom claire.gachon(a)sams.ac.uk Skype contact : claire.gachon Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/claire-gachon <http://www.sams.ac.uk/claire-gachon%0b>+++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS Research Services Ltd a Limited Company (SC224404). All Companies in the group are registered in Scotland and share a registered office at Scottish Marine Institute, 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.

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[Beg-bogas] trac tickets
by Lieven Sterck 05 Nov '12

05 Nov '12

dear bogasers/orcaers, the BOGAS trac has been moved and renamed to orcae. you can find the new trac here: http://psbsvn01/trac/ORCAE/ and to remind you all: also the bogas svn has been shut down!! so please remove your local copies and/or switch it to the orcae svn!! you can checkout a new orcae instance from http://psbsvn01/svn/ORCAE/ thx & enjoy, L. -- ============================================================== Lieven Sterck, PhD 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(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 05 Nov '12

05 Nov '12

2012/11/05 15:55:07 An error occured connecting to the database server Error message below: No config found for genome 'Catro' and release ''! at CheckAndStartBOGASupdate.pl line 76

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 05 Nov '12

05 Nov '12

2012/11/05 15:51:37 An error occured connecting to the database server Error message below: No config found for genome 'Catro' and release ''! at CheckAndStartBOGASupdate.pl line 76

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 01 Nov '12

01 Nov '12

2012/11/01 15:44:53 An error occured connecting to the database server Error message below: No config found for genome 'Ostlu' and release ''! at CheckAndStartBOGASupdate.pl line 74

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 01 Nov '12

01 Nov '12

2012/11/01 15:41:40 An error occured connecting to the database server Error message below: No config found for genome 'Ostlu' and release ''! at CheckAndStartBOGASupdate.pl line 74

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 01 Nov '12

01 Nov '12

2012/11/01 15:38:25 An error occured connecting to the database server Error message below: No config found for genome 'Ostlu' and release ''! at CheckAndStartBOGASupdate.pl line 74

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 01 Nov '12

01 Nov '12

2012/11/01 15:35:13 An error occured connecting to the database server Error message below: No config found for genome 'Ostlu' and release ''! at CheckAndStartBOGASupdate.pl line 74

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