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.
Goals/Steps
- tblastn our genes against the databases
- isolate the sequences of our hits
Blast Codes
- 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
- 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
- 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
- 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
