0
$\begingroup$

I am trying to narrow down the possible search criteria from an RNASeq experiment. I already have the cds sequences so I took these and used Blast+ program to blast the data against itself to find sequences that were the same.

From what I have read the E Value is based on the database size. My database only has ~27,000 sequences in it, does this mean that only exceptionally low E values will be relevant to me? Are there any other criteria I should search for before writing the program to eliminate similar sequences?

$\endgroup$
  • $\begingroup$ What are you mapping to the database- RNAseq reads? How long is the query? $\endgroup$ – WYSIWYG Aug 19 '15 at 5:21
0
$\begingroup$

Going by an e-value or bitscore cutoff will give you possible homologs, but it sound like you want to remove redundant sequences. If you want to cluster and combine similar sequences to make a smaller database, you could just go via sequence identity using something like CD-HIT. This, for example, is what's done to produce the UniRef set from the UniProt database.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.