Update INFOGENE: 23000 human genes; 15 divisions: mouse,pombe,fugu,Zebra fish,etc

Victor Solovyev solovyev at sanger.ac.uk
Tue Aug 31 04:30:24 EST 1999


Update INFOGENE: 23000 human genes; 15 divisions: mouse,pombe,fugu,Zebra
fish,etc
             (DATABASE of Eukaryotic GENES)

	http://genomic.sanger.ac.uk/infodb.shtml

in Update Included organisms from major Genome projects: Fugu, Zebra fish,
S.pombe

Human infogene file includes about 17000 complete (!) and 23000 partial
 genes, 66000 complete and 34000 partial coding regions, 55000 exons, about
40000

Included Drosophila melanogaster ADH 2.9 MB genomic region automatic annotation
using FGENES and FGENESH: Fgenes predictions, Fgenesh predictions, CGG1 -
summary prediction using both mention above and std3 - manual annotation based
on
experimental data (some computational) by Ashburner et al. (1999).
  This example shows problems with genomic annotation: 90% of actual coding
sequences predicted accurately, but exons often combined very different
from real genes.

   It is available at   http://genomic.sanger.ac.uk/infodb.shtml
             Computational Genomic Group WEB server

Divisions included:

Human genes data
Other Primates genes data
Mus musculus genes data
Other Rodenta genes data
Other Mammalia genes data	* New
Danio rerio genes data		* New
Fugu rubripes genes data
Other Vertebrata genes data
Drosophila melanogaster genes data
Caenorhabditis elegans genes data
Other Invertebrata genes data
Saccharomyces cerevisiae genes data *New
Schizosaccharomyces pombe genes data
Arabidopsis thaliana genes data
Other eukaryotes from GB *.pln genes data
Annotation of Drosophila Melanogaster 2.9 MB ADH region *New


- You can save an Infogene record using Action menu and Obtain Infogene
locus option (with or without sequence)
- Realized search of context (select Search filds (among many specific
  lines of Infogen database) and print your word in left down corner)
  For example you can find all genes which have start of transcription
  annotated in GeneBank: Select Context in Option menu,
  select onlt TSP field in SearchFilds, put * in search window and Enter.

To see all information about a gene in the locus:
    Put mouse pointer to gene block
   in upper window and push and keep right mouse button
   (shift key + push and click right mouse button will permanently
    show this information)
LocusInfo button will show a head of locus which shows how mane GenBank
entries included in it.
   (More details see Help in Java window!)

-- 
Victor Solovyev
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
Email: solovyev at sanger.ac.uk  http://genomic.sanger.ac.uk
Phone: 44-1223-494799  FAX:   44-1223-494919




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