Chromosome 2 and 4 of Arabidiosis thaliana Gene Predictions

Victor Solovyev solovyev at sanger.ac.uk
Tue Feb 29 00:29:56 EST 2000


Chromosome 2 and 4 of Arabidiosis thaliana Gene Predictions
===================================================================
 are available at: http://genomic.sanger.ac.uk/inf/infodb.shtml
  under CGG genomics WEB server:  http://genomic.sanger.ac.uk/    

 Even the best Gene predicton programs produce 20-25% different results,
therefore some new genes might be identified using several algorithms.
We present predictions made by Fgenesh program (Salamov,Solovyev,1999)
for
whole Chromosomes 2 and 4 in Ifogene database. The improved version of
the program
can be run on the whole chromosomes.
    You can visually inspect
predicted genes and see which have protein and EST similarity for each
predicted exon. 
 
 Also, you can ftp data for your further analysis! 
                 
   Chromosome 2 predicted genes and similarity data in INFOGENE format 
   Chromosome 4 predicted proteins in fasta format 
    
Due to high accuracy exon prediction and significantly less accurate
assigning 
exons to a particular gene, exon sequences itself present value to
experimental 
gene verification or Other projects 
               
  Visual representation of Predicted genes as well as ALL KNOWN GENES
could be 
seen in gene centred database INFOGENE through Java viewer.
    This database includes genes constructed often from many GenBank
entries, 
release 114.

Divisions with separate collections for model organisms include:

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
Oriza Sativa genes data
Zea Mays genes data
Other eukaryotes from GB *.pln genes data
Annotation of Drosophila Melanogaster 2.9 MB ADH region *New
Annotation of human Chromosome 22



- 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 many GenBank
entries are used for gene description
  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 many GenBank
entries are used for gene description





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