Difference between revisions of "Leland & Will"

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(Goals/Steps)
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== Goals/Steps ==
 
== Goals/Steps ==
 
# tblastn our genes against the databases
 
# tblastn our genes against the databases
# isolate the sequence results of our hits
+
# isolate the sequences of our hits
  
 
== Blast Codes ==
 
== Blast Codes ==

Revision as of 00:37, 16 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.

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;

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