The result is a visual tree of the matches. It is possible to get more details by clicking on one of the tree leaves:. It looks like you're using Internet Explorer 11 or older. This website works best with modern browsers such as the latest versions of Chrome, Firefox, Safari, and Edge. If you continue with this browser, you may see unexpected results. Looking at the section "Sequences producing significant alignments" we see: Amino Acid Protein Result Nucleotide mRNA 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.
Note that the first match is a synthetic construct that is, the sequence was computationally derived and is not associated with any organism :. Clicking on a protein name displays the pairwise sequence alignment and links to additional information about the protein and its associated gene if available.
For the pairwise with dots for identities display, any differing amino acid in the subject sequence will be displayed in red:. Once you do this, your search strategies should appear in the Saved Search Strategies tab. Object: Starting with two or more sequences, compare them and find the differences. This will search for nucleic acid sequences from humans with the word "mitochondrion" in the title. Mitochondrial DNA is often used in evolutionary comparisons because it is inherited only through the maternal lineage and changes very slowly.
These are high-quality sequences that have been curated and annotated by NCBI staff. There are three Reference Sequences for the mitochondrial genome in humans: one for modern humans Homo sapiens , one for Neanderthals Homo sapiens neanderthalensis , and one for Denisovans Homo sp.
To compare sequences, check the box next to Align two or more sequences under the Query Sequence box. You should see two results, in which the query sequence modern human is compared to one of the subject sequences, Neanderthal or Denisovan. Click on the name of the first result Homo sapiens neanderthalis.
You should see a base-by-base comparison of the two sequences in two lines. The top line is the query sequence modern human. In the second line, representing the subject sequence ancient human , bases where the subject sequence is identical to the query sequence are replaced by dots, and bases where the subject sequence differs from the query sequence appear in red.
Scroll down to the first coding sequence CDS. The CDS regions are displayed in four lines: the first line shows the amino acid translation for the query sequence modern human on the second line. The third line is the subject sequence ancient human , and the one below shows the amino acid translation for the subject sequence.
Note that there are two additional amino acids, M methionine and P proline , at the beginning of the protein sequence in modern humans compared to Neanderthal.
This is due to the substitution of T thymine at position in the modern human sequence for C cytosine in the analogous position in the Neanderthal sequence. Note as well that the substitution of A adenine at position in the modern human sequence for G guanine in the Neanderthal sequence results in an amino acid difference in the protein sequences.
Below is the output of clicking on the much less significant potato hit. Only a very short stretch is present over which the sequences are aligned, and even then there are nucleotides which differ between the two sequences. Methodologies and Computation.
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