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I blasted a nucleotide sequence of telomerase reverse transcriptase subunit against the transcriptome of a sea star with hope of finding homologs. Now, since this is such a common protein, I should definitely have some good hits, but what I want to know is if this splice variant is present in the sea star as well. However, when I blast it with the SRA BLAST tool on ncbi I only get very short fragments hits, most no longer than 20 bp and the sequences are very far apart. Results ranging between the two below:
Max score Total score Query cover E value Ident
46.4 46.4 1% 0.083 93%
41.0 41.0 1% 3.5 93%
Query: GenBank: JF693290.1
SRA experiment set: SRX254727
I used default settings and "Somewhat similar sequences" (there were no hits with "Highly similar sequences").
Is there something I need to think about when I blast against an SRA experiment? Some settings or something? (I'm qute new to this) Or what could be the explanation of the lack of findings?
Cheers
Max score Total score Query cover E value Ident
46.4 46.4 1% 0.083 93%
41.0 41.0 1% 3.5 93%
Query: GenBank: JF693290.1
SRA experiment set: SRX254727
I used default settings and "Somewhat similar sequences" (there were no hits with "Highly similar sequences").
Is there something I need to think about when I blast against an SRA experiment? Some settings or something? (I'm qute new to this) Or what could be the explanation of the lack of findings?
Cheers