Gene Prediction

 

genescan     http://genes.mit.edu/GENSCAN.html

genemark     http://opal.biology.gatech.edu/GeneMark/

 

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Assignment 1:

  1. Mouse tutorial starts with a portion of a mouse genomic sequence.
  2. Blasts against celera to find additional?  Annotated?
  3. Select “complete” genomic sequence (interest.seq) and submit to gene prediction servers:
  4. Genescan and genemark
  5. Compare results of predicted exons.
  6. Compare results to known.

 

 

Mouse blast tutorial: 

 

Gene prediction tutorial: 

 

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Assignment 2:

Try a few other Gene prediction servers

How do they compare to the previous?  (Note use any from this list and the list below.)

 

Grail :   http://compbio.ornl.gov/                   results:  grail-out-01.htm

BCM

BIMCORE PISE:  http://www.bimcore.emory.edu/Pise/

PISE :  Genscan                                            results:  genscan_out.htm

PISE :  GrailClient                                            results:  grailclnt_out-01.htm

PISE :  GetORF                                            results:  getorf_out.htm

Orf finder     http://www.ncbi.nlm.nih.gov/gorf/gorf.html  (runs really fast, questionable)

 

 

 

Lists of other Gene Prediction servers:

 

1.    REVIEW this page (Gene Identification and Repeat Analysis) 

   http://cmgm.stanford.edu/classes/genefind/

 

2.     Gene finding and intron splice site prediction     

http://www.cbs.dtu.dk/biolinks/pserve2.html

 

 

 

microbial gen prediction   http://compbio.ornl.gov/generation/

 

gene prediction                http://www.bork.embl-heidelberg.de/genepredict.html

 

 

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Assignment 3:

 

 

Did you find the initial start sequence of the gene?

If so submit the potential promotor region for prediction of transcriptor factor binding sites.

 

Transcription factor predictions:

 

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