I think my question yesterday wasn't very clear, sorry. What I'm on about is the default effects of /gene, /product, /note and /label. For instance:
misc_feature 1..578
/note="sequence a; terminal redundancy"
repeat_region 1..11247
/note="TRL; inverted"
/rpt_type=terminal
CDS 970..1905
/codon_start=1
/gene="this is a gene"
/product="this is a product"
/label="this is a label"
/note="this is a note"
/protein_id="NP_783767.1"
/db_xref="GI:28373215"
/translation="MPATDTNSTHTTPLHPDAQHTLPLHHSNTQPHVQTSDKHADEEH
RTQMELDAADYAACAQARQHLYDQTQPLLLAYPNTNPQDSAHFPTENQHQLTHPLHNI
GEGAALGYPVPRAEIRRGGGDWADSASDFDADCWCMWGRFGTMGRQPVVTLLLARQRD
GLADWNVVRCRGTGFRAHDSEDGVSVWRQHLVFLLAs far as I can see, only /gene annotates the turquoise CDS bars. /note gives annotation visible in the feature table. /product and /label don't automatically do anything (like protein_id or db_xref). Is this what should be seen or have I misconfigured something? (I'm running Artemis 5 on a Compaq Tru64 - I've considerably hacked about with the Graph and Run menus, but not done anything that I think would damage the display).
Cheers Derek
At 17:13 14/01/2004 +0000, Stephen Bentley wrote:
I'd globally swap /product for /label
Derek Gatherer wrote:Hi
I have a genome annotated with /product and /label in the feature table.
eg:
primer_bind 80929..80945
/note="PRIMER U54s8"
/label=U54s8
primer_bind complement(81373..81393)
/label=U54P5
/note="PRIMER U54P5"
CDS complement(81703..84423)
/note="envelope glycoprotein; HSV-1 UL27 counterpart; gB"
/codon_start=1
/product="UL55"
/protein_id="NP_039989.1"
/db_xref="GI:9625740"
/translation="MESRIWCLVVCVNLCIVCLGAAVSSSSTSHATSSTHNGSHTSRT
TSAQTRSVYSQHVTSSEAVSHRANETIYNTTLKYGDVVGVNTTKYPYRVCSMAQGTDL
IRFERNIICTSMKPINEDLDE
How can I make those /label annotations appear in the viewer underneath the corresponding CDS? So the gene above would be instantly visible as UL55, and the nearby primer binding site as U54P5?
I tried "Automatically Create Gene Names" and "Fix Gene Names", but the first wanted to add new annotation and the second seemed to assume that all gene name were "CDS" (and gave an endless series of popups saying that CDS overlapped with another gene called CDS).
As always, all help gratefully received.
Cheers
Derek
_________________________
Derek Gatherer Ph.D. Cert.Ed.
Computer Officer
Institute of Virology
Church St.
Glasgow G11 5JR
Phone: +44 141 330 6268
Fax: +44 141 337 2236
Email: [EMAIL PROTECTED]
Website: http://www.vir.gla.ac.uk
-- ******************************* Dr. Stephen Bentley Project Manager Pathogen Sequencing Unit Wellcome Trust Sanger Institute *******************************
