Difference between revisions of "Leland & Will"
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- Lignin: role with phenolics, wine, etc. | - Lignin: role with phenolics, wine, etc. | ||
| + | == Files == | ||
| + | #'''454 Genes''' | ||
| + | ##454 Genes [[File:P450_GENES_protien_bb_latest.txt]] | ||
| + | ###Only the Forward genes. (no rev comp) [[File:P450_GENES_protien_bb_latest_forward.txt]] | ||
| + | ##Forward genes in blast against EST database [[File:P40_est_algined.txt.zip]] | ||
| + | #'''Illumina Genes''' | ||
| + | ##Illumina P450 Amino Acid [[File:p450Protein-Illumina.txt]] | ||
| + | #'''Presentations''' | ||
| + | ##Fast presentation [[File:FastPresp450.pptx]] | ||
| + | ##Final Presentation [[File:Final_Presentation.pptx]] | ||
| + | #'''Data for Figures''' | ||
| + | ## [[File:p450Counts.zip]] | ||
| + | ## [[File:PPT_seq.txt]] | ||
| + | #'''Figures''' | ||
| + | ##[[File:P450HitsGraph.xlsx]] | ||
| + | ##[[File:ScaffoldGeneFigure.pptx]] | ||
| + | == Goals/Steps == | ||
| + | # tblastn our genes against the databases | ||
| + | # isolate the sequences of our hits | ||
| + | # visualize with artemis | ||
| + | # try to identify introns/exons | ||
| + | # Choose a p450 | ||
| + | # Get every hit that we have for that gene | ||
| + | # ClustalW align them against our p450 | ||
| + | |||
| + | == To Include in Final Presentation == | ||
| + | # How many p450 hits we got?... How many would we expect | ||
| + | # Graph of hits, Scaffold figures | ||
| + | # Easily totally align by using gene as root comparison, and aligning all other fragments to that. | ||
| + | |||
| + | == Blast Codes == | ||
# Easier Blast | # 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 | /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 | # 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 | /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 - [http://www.p450.kvl.dk/TFAfiles/AtP450PROT.tfa 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 | ||
Latest revision as of 14:05, 14 April 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
- 454 Genes
- 454 Genes File:P450 GENES protien bb latest.txt
- Only the Forward genes. (no rev comp) File:P450 GENES protien bb latest forward.txt
- Forward genes in blast against EST database File:P40 est algined.txt.zip
- 454 Genes File:P450 GENES protien bb latest.txt
- Illumina Genes
- Illumina P450 Amino Acid File:P450Protein-Illumina.txt
- Presentations
- Fast presentation File:FastPresp450.pptx
- Final Presentation File:Final Presentation.pptx
- Data for Figures
- Figures
Goals/Steps
- tblastn our genes against the databases
- isolate the sequences of our hits
- visualize with artemis
- try to identify introns/exons
- Choose a p450
- Get every hit that we have for that gene
- ClustalW align them against our p450
To Include in Final Presentation
- How many p450 hits we got?... How many would we expect
- Graph of hits, Scaffold figures
- Easily totally align by using gene as root comparison, and aligning all other fragments to that.
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
