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...
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-- ============================================================== 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 ==============================================================