Matt:LabNotes/2014-2-3: Difference between revisions
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>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...") |
>Mzcai |
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blastall -i primers_7nt.txt -d RNAsequences.fa -p blastn -o result_7.txt -W 7 | blastall -i primers_7nt.txt -d RNAsequences.fa -p blastn -o result_7.txt -W 7 | ||
* | ====Results==== | ||
*BLAST of 10nt primers | |||
**Wordsize 7: [[File:Result_wordsize7.txt]] | |||
**Wordsize 8: [[File:Result_wordsize8.txt]] | |||
**Wordsize 9: [[File:Result_wordsize9.txt]] | |||
**Wordsize 10: [[File:Result_wordsize10.txt]] | |||
*BLAST of 7nt primers: [[File:Result_7.txt]] | |||
====Conclusion==== | |||
*Looking only at primers that match at the 3' end, the only alignments are to RNA pseudogenes | |||
**1000nt RT primer has NO alignments of any kind | |||
*Therefore it is unlikely that it is because of high amounts of rRNA primary rolonies that 1000nt shows so much signal |
Latest revision as of 01:37, 8 February 2014
BLAST RT RAB7A primer sequences against rRNA[edit]
- 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[edit]
- 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[edit]
- BLAST of 10nt primers
- Wordsize 7: File:Result wordsize7.txt
- Wordsize 8: File:Result wordsize8.txt
- Wordsize 9: File:Result wordsize9.txt
- Wordsize 10: File:Result wordsize10.txt
- BLAST of 7nt primers: File:Result 7.txt
Conclusion[edit]
- Looking only at primers that match at the 3' end, the only alignments are to RNA pseudogenes
- 1000nt RT primer has NO alignments of any kind
- Therefore it is unlikely that it is because of high amounts of rRNA primary rolonies that 1000nt shows so much signal