The E value depends on the length of the query sequence and the size of the database. Personally, I use an E value of 0.001 for querying of large databases, then I look at % match to explore the hits I recovered.

I typically only use BLAST to search for specific sequences in my data, or when I want to quickly see if a sequence of interest is in the NCBI database (BLASTing via their web portal).

Just as an aside, in case you are using BLAST to assign taxonomic hypotheses to your sequences...you may want to consider some of the software that breaks a query sequence up into k-mers and matches those to a well-annotated training database (e.g. SINTAX). This is because there are a lot of poorly/wrongly annotated sequences on NCBI.

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For more on E values see the Palumbi lab's website: http://sfg.stanford.edu/BLAST.html

They suggest an E value of 0.001 to start, followed by a more stringent E value to find best hits.

Also, here is what NCBI's website states:

Link: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ

"Q: What is the Expect (E) value?

The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.

The lower the E-value, or the closer it is to zero, the more "significant" the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence. These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance. For more details please see the calculations in the BLAST Course.

The Expect value can also be used as a convenient way to create a significance threshold for reporting results. You can change the Expect value threshold on most BLAST search pages. When the Expect value is increased from the default value of 10, a larger list with more low-scoring hits can be reported."

I would suggest to go for least e-value. E value of 10 sounds very high for the sequence matches. Also, check others parameters like coverage and scores. I have ofter seen if the e-value is very high, there is generally very little query coverage.

The E value depends on the length of the query sequence and the size of the database. Personally, I use an E value of 0.001 for querying of large databases, then I look at % match to explore the hits I recovered.

I typically only use BLAST to search for specific sequences in my data, or when I want to quickly see if a sequence of interest is in the NCBI database (BLASTing via their web portal).

Just as an aside, in case you are using BLAST to assign taxonomic hypotheses to your sequences...you may want to consider some of the software that breaks a query sequence up into k-mers and matches those to a well-annotated training database (e.g. SINTAX). This is because there are a lot of poorly/wrongly annotated sequences on NCBI.

--

For more on E values see the Palumbi lab's website: http://sfg.stanford.edu/BLAST.html

They suggest an E value of 0.001 to start, followed by a more stringent E value to find best hits.

Also, here is what NCBI's website states:

Link: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ

"Q: What is the Expect (E) value?

The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.

The lower the E-value, or the closer it is to zero, the more "significant" the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence. These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance. For more details please see the calculations in the BLAST Course.

The Expect value can also be used as a convenient way to create a significance threshold for reporting results. You can change the Expect value threshold on most BLAST search pages. When the Expect value is increased from the default value of 10, a larger list with more low-scoring hits can be reported."