i recently got my dna sequence results, i performed a blast for the sequence on NCBI, did alignment with aliview and constructed a phylogenetic tree but i encountered some issues.
1. with similar e value and number of hits, how do i select from the results from the blast
2. what is the inference to be gotten from alignment and phylogenic tree
p.s i'm a new researcher
Read this
https://www.researchgate.net/post/What_does_E_value_in_BLAST_actually_indicates
1) Lesser the E-value, Better is the Hit you got in the alignment.
2) Alignment will help you in comparing of your query sequnce with the sequences in the databases. By looking the alignment section you can notice the matches, mismatches (substitution mutation ) and gaps (due to insertion/deletion mutation) among the query and database sequences.
3) Phylogentic trees are helpful in determination of evolutionary relationship among the compared sequences. The pattern of branches graphically depicts the relationships among your sequence with other sequences which you select to build the tree.
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.
BLAST helps us to identify sequence similarity across genomes, to identify right primers for research work, to understand if there are any mutations in the sequence of interest.
Thank You!
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