Matt:LabNotes/2014-2-3
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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 are complementary to some really high abundance transcripts
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