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8.1 years ago
nasromer2191989
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20
I use fasta file that contain miRNA sequences as query against EST & GSS database in local blastn to search for similarity sequence but the problem I could not manage to change the sequence to miRNA back to check if it pick new sequence that similar to the query sequence. this the result how it look like
ref|NR_030619.1| Homo sapiens microRNA 543 (MIR543), microRNA Length=78
Score = 145 bits (78), Expect = 1e-32
Identities = 78/78 (100%), Gaps = 0/78 (0%)
Strand=Plus/Plus
Query 1 TACTTAATGAGAAGTTGCCCGTGtttttttCGCTTTATTTGTGACGAAACATTCGCGGTG 60
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Sbjct 1 TACTTAATGAGAAGTTGCCCGTGTTTTTTTCGCTTTATTTGTGACGAAACATTCGCGGTG 60
Query 61 CACTTCTTTTTCAGTATC 78
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Sbjct 61 CACTTCTTTTTCAGTATC 78
anyone have an idea
Not clear what exactly you are asking. Can you clarify?
If you used known miRNA as a "query" then the "hit" should give you the name of the sequence from the EST/GSS database. What command did you use to run the local blast?
If you want to play with the blast results, it can be easier use tabular output (
-outfmt 6
). Hope this help in whatever you want to achieve (not clear for me in your post).The command line that I use
blastn -db database file -query my/file (known miRNA) -out result file name .out I am new user of blast so while I use miRNA sequence as query What it sould be the result? is it miRNA that similar to query miRNA?
however I would like to do prediction of miRNA based on the file that obtained from database if it is possible
anyone have an idea