In a number of suspected new species/genus records (mangroves), % query cover is very low,
Felix
Query coverage is the percentage of your sequence aligned to a sequence in genbank. This is the effective size of the sequence been compared. Low query coverages results from different ways: your sequqnces is to short, your sequence has good size but sequences on genbank are to short, or your sequence is to different from every thing in genbank that only a part of it can be compared. The smaller is the query coverage, less data (nucleotides) are been compared and the chance or error (E) is higher. So if the E value of the query is =0 it dosent matter if the querry coverge is
Dear Felix
The lower % Query Coverage of your query sequence indicates that the overlap
with the reference sequence is very low. However, higher % Identity indicates that whatever sequence which overlapped matched very well.
As you are saying your percent identity is around 95%, I would like to know how many base pairs (bp) does your query sequence have?
If you can share the screen shot of your BLAST results, it will be much better to understand your problem.
Thank you
I have a question to the expert
Does 79 % query cover with 29 % sequence identity indicate significant match?
I have provided a screenshot of my BLAST results based on some sequencing work I have done recently with regards to verifying the cloned gene ANXA5 in plasmid pCMV-His-ORF. It says 77% query cover, E value 0 and Ident 99%. So is it correct to say that the plasmid sequenced has a 99% identity in a 77% coverage of the complete ANXA5 gene sequence? How should the BLAST results be read? Thank you.
To Rekha Chaturvedi: Generally % identity should be considered if its above 35% and % coverage is above 80%. In your case, 79% coverage is in acceptable range whereas 29% of sequence identity cannot be considered as good match. Thanks.
HI. @Sunil, pls can you further clarify to us based on the screenshot provided above by @Eugene ??
hello, What is the percentage used when searching plasmids or phages by BLAST?
I have a question related to the this discussion and I the experts on this subject can provide an answer....
A genetic barcoding result I sent came out as
1) 99.68% match /100% cover for BLAST
2) 100% match/97% cover for BOLD.
Which of the two has higher match?
Thank you in advance!
Hello,
I have the same issue, good %identity but bad coverage, I am running BLASTn against genomes. Does anyone know if the same applies whwn I blast against genomes?
I wanna ask for this sequence:
GCAAAAGCTCAAATTTGAAATCCCCCGGGAATTGTAATTTGAAGAGATTTGGGTCCGGCCGGCRGGGGTTAAGTCCACTGGAAAGTGGCGCCACAGAGGGTGACAGCCCCGTGAACCCCYTYAAMGCMCTCATCCCAGATCTCCAAGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATACCGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGCACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGCTTGCAAGCAGACACTTAACTGGGCCAGCATCGGGGCGGCGGGRARCAAAACCACCGGGGAATGTACCTTTCGAGGATTATAACCCCGGYCYYWAYTYCCWYRYYRCCCCGAGGCCTGCAATCTAAGGATGCTGGCGTAATGGTKGCARGTCGCCCGTCTTS
When I blast this sequence the identities come from lower identity why?
actual problem is sorting of the BLAST sequence according to percentage identity but automatically it goes by E value. Please help me !
Your question is a bit unclear. Low identity to your organism of interest or in general? It can be due to many reasons. Your fragment has been correctly sequenced? Is that confirmed by forward reverse comparison? Is your sample a novel individual? The gene that you used is common for your sample?
- Badges
- Science method