GreenGenie2

Welcome to the GreenGenie2 example submission form!

Reference:
Kwan AL, Li L, Kulp DC, Dutcher SK, Stormo GD: Improving Gene-finding in Chlamydomonas reinhardtii: GreenGenie2. BMC Genomics 2009, 10:210

Example DNA sequence (uneditable): BLD2
>BLD2 GGGACATTCGTATCTTACAGTGTGTTGACATGTGCGGGATACAGTATGCGCCCAAGCACG CTGCCCTGTCTGGGGTGCCCGACAGCGCGCCGGTTGCGACTTTGACCATGCAAGTGATGC AACCCTACCCCTCGGGCTAGACTGCTGGGCTTGACAGGACTCATCATGCGTTCACCCGCC GCCACAACCAAGCGGTTCTCGTTCCTTATTCCTTACTACTCCAGGTCTCCACGCCCCAAC CACCTCCACTGCCATGCACAGAACCTGGGCCCGCCACCGTGTCCTCACCCCGGCCCCTCT GCCGCGTCCAGCGTACATAGTACGTACACTGCTCCATGGTCCTTGCAGCCCCGCCATCAG GAGCCTGCCCGGGTCGCGACAACGCCCCTTCCACCCCTGCCCGCCCACCACCAATCAACA TCCCCGCGCCCAGCAGCCGCCCACCTCACAATGCACTGTGGCTCACGGCGTCGCTGAGCC GGGATCCGGAGAGTCACCGAAGGCGCCTCACGCGCTACACTTTTACCTCACGCAGTATCC ACACGCGCCTCTCCGCATGGCCGCGCGCATCACGGCAGGAAGGACAACCCTCGCGGCCGC AGGCGTGTGAGCGGCGGCGCCTGTGTGGCTCCTTCCAGGGCTCGGTACTGCGCCGTGAGG TCGCCCACCACCTCCATGGCCGAGGTGAAGCCGCCCGGATCCATGTACTGCTCGTAGTGG TGCGTGTAGAACCTGCGGGAGGCGGCAGGAGGGAGGAGGAGGAGGATAAGGGAGGAGAAG GCAGAGCGTGTTGGGGGTGGCGGGCGGGCGTGGGTGTCGGGATTGGACGGAGGACCCCCA CGCGGCCGCCGCACCTGCGCTTGTACAGCTTGTCGAACCGCTCCCTCATGGTCGTGAAGG TATGTGCGATGGCTGTGTTGTTGGCCAGACACAGCAGACCGAAGGGGCAGCCCACGGGCG GCGTGCTGCAGATACCCAGCTTGAAACCCTTGGGGATGACACAGGGGTTCACACGGGAGG GGACAAGAGGTATGAGAGGGGCGCAGGCGCCAGTGCGATGCGGCGGGTTGAAGGCCGGTG CTTGCTCACGGCTCATGCGCTCAGGTGGCAAGGCGATGGGTACCAGCAACATGATGCACA GAACGGGACCAGGCTTGGCGACCTTTGACCGCACGCGTCCACGTGCGCAGCCCGACCCTC CAGCCCCGCACGCCCCTGAACCCGCCCCTGAACCCGCCCCAACCACCGAGCGTCCCCTCA TTGTGCACCCCAACACTACCGCCCCACGCCACCATCCCACGCCACCACAAACGCACCTCG CTGTTCCAGTGCACCATCTTGAGCTGCGGTCTCAGGCGCGCCACGTTGCGGTTGATGTCG GCCATGGTGGCGGTGGGGCCGCGCGCGATGAGGCCGCACGCCAGGTAGGTGGCGGCCCGC GGGTCGGCGCGGATGAGCTGGTGCTCCCGACTGAACACGTCGCCAAATACCTGGGGGGTG GAGGGCGGATGGGGTGTCAGGGGCTTACATTTGTCATAAATTGGGGGCGAGGCGTGAGCG AGGTGCGAAAGGCCAGAACCGAAACAGCGGCTGAGGGTGGCTGCTTGGGTTCCGTGGCGT GTAGCCGGTGCACGTGGCTGGTGGAGGCTCCAGGCAGGATCAGAGCGTCATGAAAGGCAG GCCGCGGCATATCGAGCGCCCCTGCCACTGCACCCGGGCCACTCGCACCTGGTCCAGCGT GCGCGGCTGCAGCGCCAGCGCCGCCGCGGCGCGGCCCACGTCCTTGTCCTTGGGCGGCGG CTGCAGCGGGCTCATGCTGCTGAGCAGGAAGTGCATGCGCGGGTAGGGCACCAGGTTCAT GGTGATGTCGTTGAGGTCCACGTTGAGCGGGCCCTCGAAGCGCACGCTGGCCGTCAGGTG CAGCAGCAGGCTGGCGGCGACGCCGTTCATGGAGTCAAAGGGCTTGCTGCCGCCGCCGCT GCCTTTGAGGCCGGAGACGGCGGAGGCGGCCGCGTCGGCGGCTGCGGGGTAAGGAGGCGG CAATGGCCAGCGCGCAGATGTTGTCAAGTGGCTACTGGGAGCATTGCAAAGTCCCAACAT GCCTGCAGGAGGGCCCTGGCGCGCAACTCCACCTTCCATGCGGCCATACCCCGTGAGGCC GTGACCCCGCCTGCCCCCACAGCTCCCACAGCCCCCTCCGGCCGCCGCCTACGGCACCCC CACGCACTCCACGCCCCCGCACCCTCTCACCCACGCACCCGCTGCCCGGTCCCGCGCTGC CTCCGTGCGGTTGACGATGTCGATGAGCGCCTGGTTCTCAATGGGCAGCACGCAGTCGGC GTGCTCCACCAGCTGCCCCAGCGCCAGCATGGCGTTGTAGGGCGAGGTGACCACGTCGTC GTCCTCGGAGGGAAACACGCTGCCCGTGAAGCGGAACACGCCGGGGAACTCATCCTGCAG CGGGGGGTGGGGTGGGAGGGGTGGACAGGGGAGGGGAGGGGAGGAGAGGAGAGGGTGGTG TGAAGTTGAGTGGCAGGTTGTGGCGTGGGCCGAGTGAAGAGATTGTCCCAACGGCCCGAC AGCTGCTGCATTGTGATTGCCATGACCTCTACGAAGACAGCAGCATACAGCCATACACAC GCATACGGCGTCGTCTGAGCGGGCGTCCGCTTCGTTTTTTAACACACACAACCCTTGTGC TCTCACTCTCACTCTCACTCTCACACACACACACACACACACACACACACACACACACAG CCCCCTGCCCCCTCCATGCTCACCGCCAGCATGCGCACAATGTAGGTGCCCACGCCACTG CCCGTGCCGCCGCCCAGCGAGTGAAGCACCATGAAGCTCTTGGGGAGCGGGAGGAAGCGG AACGGGTCGACGAGAGGTGTCACTGTGTCAGCCAGGCCCCAGGCGTGGGCTCCAGGTTCC CTTTGGCTTAGTTCCCCGTTGTCACCACCACGCGCTTCCCACCCGCCCTCCCCTCTCGCT GCCCCCGCCCCACGCCCCACGCGGCCACGCCCCCACGTGCCCACCTGCAGCGAGTCACAG TCCTCGGCGGTGAGTCGTATCTTGTCCAGGATGGCGTCGTGGTAGCGCGGGCCGTACTCG TGGTGCCCGTGCGCCCAGTTGTTGCCGGCGCCGCTCACGTCGCTCACCAACTGCCGCGTG TCCAGCACCTCGCCCAGCGGGCCCTGAGGCGGGAGGGGGGATGGGAGGGGGGAAGGGGAA GGAGATGGGAAGGGGACGGGAGGGTGGGAGGAGCGGGCAGCAGCGCACCGGCGGTCAGCG GCAAGTGAGATGAGAGGTGGAAGCGGCAACGGCAGTGTGTGTGTGTGTATGTGTGTGTGT GTGTGTGTGTGTGTGTGTGTCTCAGCATGCATGCGCCATACGTGCGCGGGGCAGGTGACC GTAATGAGAGCGGTATGGGGCTGTACTGCTATGCTCCGCTATGCACACGTGCCAAACACA CCGCTGCACCCGCCACGCCGAGTACACATGCGTGCTCAACACTCAGGCCCCCCCACTCAG GCCCCCCCACACACCTTGAGCATCTCATTGATGACGCCACACTCCATGTCCACAATGACG GACCGGGCCTGGGGGCCAGGGCGGGGCGGGTTGGGATGCGTCATGCGTGGAAGTAGGCTG GTAGGGGGTGCACCGCCAAGCACGCCTCCAGCGCCAAACCCAGCAGCACCACAACCCAGG GCGATCACGCTGGCCCCCTCGAACGCGACGCAATATTTCAGTGTGTCCTTGACCGGCTGG TTGTTGAGAGGCCCACCCGCTGGGCCTCCCACGCCACGTCACCCTGCCAGAGTCTGCATG CGGCTCGGTCCCTCCGCCCACTCCGCTGCCGACTCGCTCACCTTGAGTGTACGGATGGCG CCGCGGCCTTCGCCCACCGGCAGATTCCTGCAGTCACCAATATGTGTGTGAGTGCCCGTA GAGGACCCAATGGAAGGTGTCTGACGCAGTCCGCTGCACTGCCCGTGTCCTGTCACCGCC AGTGCCTGACACGCTCGCGCCACCATTCCCTCTCTCCATCCTACTCCATCCCACCCACCG CGGTGGCTCCACGCGCGTGTCCACATTGCGGAAGAAGCTGCTCAGCGCCTCGTCGTACAC GCCCTTGGTGTTGTAGGCTGCATGCTCGCGAAGCGCCAGCTCCCAGAAGCGACAGCCCAC CTGGTTGCCGCACTGGCCCACCTGGATGGTCACGAGCTCGCGCGGCATCGCCCCGCTGTA GGCTGGTGTTTCGTGTGAGGCTCCTTCCAAGTTGCAGCGCAGTGGCCGCGGCACCTGCTA TGCCTTGCTACGTTGCCGGGAACTCCATTCAATTACACAGCGCCAGGGCGTCCCGGCGCG CAATGCTGGCCCCCGCCCCCGCAGCGGCCGACAGCTGGGCCACGGCCCGTGTGGCCTAAA TGATATTTATGCAAGACGAAAGGTCCTGCAGCGACTTGTGCGTAAGAAGAAGTCACGACT AAAACGTCTCCAAGGATGGAAGAGCTTCAGAGCAAGCCTGTCATCAGTTTATCCAACGGC TCAGAGCTGGTACACGTAGCTAACCTGTTCTTTCCATGTGACAGGAACTCCTTTATGTTC CTTTGTGACCCGCAGGGTCTGCCTTGCAAAATCGACGCTCCTCTCGACTGAGCTGCATCA GTATTG [input your own sequence]

Here's an example DNA sequence in FASTA format to get you started! Note that, since this example uses the custom track feature, the example sequence provided here is the plus strand and GreenGenie2 is asked to make predictions on both strands.
Predict... one or more genes. up to one gene.
Now, indicate how many genes you expect to be in the input sequence.
Make predictions on... both strands. forward strand only.
Do you want predictions on one or both strands?
Make predictions using... Chlre3 EST assembly models. Chlre4 EST assembly models (beta).
Chlre4 parameters are provided as a potential source of alternate gene models. Short-sequence prediction performance is comparable to the default (Chlre3).
Output fasta row length? 60 90
Specify the number of characters per fasta row.
Example JGI Genome Browser Custom Track Header (uneditable)
browser position chromosome_3:3098074-3102759 track name=gg2BLD2 decription="epsilon tubulin" [input your own sequence]

You can also enter a header for the JGI Custom Track Import Tool! GreenGenie2 will adjust the prediction for you! Then, just copy the text as instructed and paste the pre-formatted GreenGenie2 prediction at JGI to see your own custom track!

The appropriate Chlre4 assembly header has already been provided for this example.

Once more, for proper automated generation of custom track code, the example DNA sequence above is from the plus strand.