It is essential to take the e value into account and l ook for homology between conserved regions- this will be evident at the protein level. A query sequence can have a low % identity, but still be a real hit. Percent identity: the % of bases that are identical to the reference genome.E value smaller than ten will include hits that cannot be considered as significant as a low e value, but if it is a divergent virus, the e value may be high. E value 10 large E value: many hits, partly of low quality.E value 0.01: Blast hits with E value smaller than 0.01 can still be considered a good hit for homology matches (ok for divergent viruses), but this is not considered a ‘good’ e value.Blast hits with an E value smaller than 1e -50 include database matches of very high quality. E value 1e-50 small E value: low number of hits, but of high quality.This metric is extremely useful for identifying real hits. The hits are automatically sorted by E value (best to worst). E value : the number of hits expected to be seen by chance.If there is an alignment with 100% identity and a 5% query coverage, the sequence is probably not that taxon. A small query coverage % means only a tiny portion of the contig is aligning. Query coverage : the % of the contig length that aligns with the NCBI hit.If you are to find taxon A in the sample report on CZ ID and run BLAST, it is possible that taxon A would not be the top hit in the BLAST table because BLAST sorts by e value. One thing to note is that CZ ID uses an algorithm equivalent to "total score" to assign taxonomic IDs.The higher the score, the better the alignment. Total score: the sum of the alignment scores of all of the segments from the sequence.It is derived from the raw alignment score the higher the score, the better the alignment. The bit-score is the required size of a sequence database in which the current match could be found by chance. Max score: the highest bit score that is calculated from alignment matches and mismatches.
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