Difference between revisions of "Leland & Will"

Revision as of 14:16, 17 March 2011

- 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. http://gcat.davidson.edu/mediawiki-1.15.0/images/3/35/Test.txt

1. Illumina P450 Amino Acid File:P450Protein-Illumina.txt

Goals/Steps

1. tblastn our genes against the databases
2. isolate the sequences of our hits

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