BLAST Results

Analyzing the results of a BLAST search, while similar, will depend on whether the original search was for a nucleotide or amino acid sequence.

Looking at the section "Sequences producing significant alignments"  we see:

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Amino Acid (Protein Result)

Nucleotide (mRNA)

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In either case, the items of interest are:

• Max[imum] Score: the highest alignment score calculated from the sum of the rewards for matched nucleotides or amino acids and penalities for mismatches and gaps.
• Tot[al] Score: the sum of alignment scores of all segments from the same subject sequence.
• Query Cover[age]: the percent of the query length that is included in the aligned segments.
• E[xpect] Value: the number of alignments expected by chance with the calculated score or better. The expect value is the default sorting metric; for significant alignments the E value should be very close to zero.
• Ident[ity]: the highest percent identity for a set of aligned segments to the same subject sequence.

These results can be helpful in identifying what the searched sequence matches and what other species have similar substances.

Clicking on the name of any of the results will. again, display different results:

 

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Amino Acid (Protein Result)

The results show the amino acid matches

Nucleotide (mRNA)

The results show the alignment of the base pairs

Compare Multiple Sequences

Another form of searching is to compare 2 sequences to each other.  The image below is from BLASTP, but the BLASTN has a similar facility.  This is activated by clicking the "align two or more sequences" link:

Taxonomy Tree

Another interesting result is the report of the taxonomy tree of the significant matching sequences.  Once again the results are similar for BLASTN and BLASTP.  The example shown is from BLASTP:

Click on the "Distance tree of results" link.

The result is a visual tree of the matches.  It is possible to get more details by clicking on one of the tree leaves: