Matt:LabNotes/2014-2-3

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Revision as of 07:38, 7 February 2014 by >Mzcai (Created page with "===BLAST RT RAB7A primer sequences against rRNA=== *From Matt:LabNotes/2014-1-31#RT_RAB7A Primers and the Number of RAB7A Primary Rolonies it seems like some sequences ar...")
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BLAST RT RAB7A primer sequences against rRNA

BLAST with ribosomal RNA

  • Used Biomart sequence retrieval tool, searched for unspliced (transcript) and used Filter = Gene: rRNA with Associated Gene Name as heading for fasta file
    • Downloaded and stored in my genome-miner as RNAsequences.fa in /RT_RAB7A
  • Built database
 formatdb -i RNAsequences.fa -p F
  • Saved a fasta file of RT primer sequences and then BLAST-ed with wordsize of 7, 8, 9, and 10
 blastall -i RT_RAB7A_primers.txt -d RNAsequences.fa -p blastn -o result_wordsize7.txt -W 7
 blastall -i RT_RAB7A_primers.txt -d RNAsequences.fa -p blastn -o result_wordsize8.txt -W 8
 ...
  • Shortened primer sequences to 7 by removing from the 5'end and BLAST-ed with wordsize of 7
 blastall -i primers_7nt.txt -d RNAsequences.fa -p blastn -o result_7.txt -W 7
  • Results