Leland & Will

- MYB transcription factors

- P450s function and role in blueberries

- cultivation of blueberry genome duplication (starting point)

- RNA

- Genome Analysis: codon bias, GC skew, pH pathways/sources, genome comparisons (Arabidopsis, etc.)

- Circadian rhythms ([1])

- GC content of exons/introns

- Lignin: role with phenolics, wine, etc.

Files

1. 454 Genes
   1. 454 Genes File:P450 GENES protien bb latest.txt
      1. Only the Forward genes. (no rev comp) File:P450 GENES protien bb latest forward.txt
   2. Forward genes in blast against EST database File:P40 est algined.txt.zip
2. Illumina Genes
   1. Illumina P450 Amino Acid File:P450Protein-Illumina.txt
3. Presentations
   1. Fast presentation File:FastPresp450.pptx
   2. Final Presentation File:Final Presentation.pptx
4. Data for Figures
   1. File:P450Counts.zip
   2. File:PPT seq.txt
5. Figures
   1. File:P450HitsGraph.xlsx
   2. File:ScaffoldGeneFigure.pptx

Goals/Steps

1. tblastn our genes against the databases
2. isolate the sequences of our hits
3. visualize with artemis
4. try to identify introns/exons

1. Choose a p450
2. Get every hit that we have for that gene
3. ClustalW align them against our p450

To Include in Final Presentation

1. How many p450 hits we got?... How many would we expect
2. Graph of hits, Scaffold figures
3. Easily totally align by using gene as root comparison, and aligning all other fragments to that.

Blast Codes

1. Easier Blast

/usr/local/ncbi/blast/bin/blastn -query arabchloro.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" -gapextend 2 -gapopen 5 -penalty -3 -reward 2 -evalue 10 -word_size 11 -template_length 18 -template_type coding

1. Easiest Blast

/usr/local/ncbi/blast/bin/blastn -query arabchloro.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" -gapextend 2 -gapopen 5 -penalty -3 -reward 2 -evalue 10 -word_size 11

1. Blast Protein vs Nucleotides

/usr/local/ncbi/blast/bin/tblastn -query AtP450PROT.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" -out p450Protien.txt -evalue .0001

1. Isolate Blast Results

blastdbcmd -entry 71022837 -db Test/mask-data-db -outfmt "%a %1 %m" XP_761648.1 1292 119-139;140-144;147-152;154-160;161-216;

Links

• http://www.p450.kvl.dk/ - complete collection of Arabidopsis P450 sites - Arab p450 protein file
• http://arabidopsis-p450.biotec.uiuc.edu/ - complete collection of Arabidopsis P450 sites
• http://arabidopsis-p450.biotec.uiuc.edu/cgi-bin/p450.pl - searchable Arabidopsis P450 database