Homology Search Results and Pairwise Alignments

The results from the sequence homology search are presented as a compact tabular view that summarizes the key alignments statistics and as expanded detail view showing pairwise sequence alignments.

Pairwise #1

The compact tabular view lists the top hits matching the query sequence. It shows the function of the gene/protein hit, corresponding genome, subject length, percent identity, percent query coverage, percent subject coverage, BLAST score, and E value. These summary statistics allow you to quickly assess the quality of the BLAST hit. For each gene/protein hit, function is hyperlinked to corresponding Feature Landing Page, which provides detailed information about the feature. Similarly, the genome name is hyperlinked to corresponding Genome Landing Page, which provides further information about the genome.

The check boxes in the beginning of every row can be used to select search results and copy them to narrative. Please note that if the search is against the gene or protein database, then the objects being copied to narrative are genes or proteins as Features. If the search is against genomic sequence database, then the objects being copied to narrative are genomes.

Pairwise #2

You can view the detailed pairwise alignments by:

  1. Clicking on the “Expanded Results” button above the table, which results in an expanded view, showing pairwise alignments for all the hits in the table.
  2. Clicking on the Right Button button in a row to see pairwise alignments only for that hit. Similarly, expanded view for a row can be toggled back to collapsed view using the Up Button button.

Pairwise #3

The key features of the pairwise alignment view include:

  1. Alignment summary – summarizes the query and subject lengths, BLAST score, expect value, number of identities, positives, and gaps.
  2. Pairwise alignment – shows the alignment of query and subject sequences.
  3. Number of matches – displayed when a search is against a non-redundant gene or protein database. This number summarizes the total number of identical gene/protein sequences currently present in all KBase reference genomes.

When the results are from the search against a non-redundant database, all identical hits are merged and only one representative hit is shown, instead of showing separate hits for every identical feature, with exactly the same score and alignment.

Pairwise #4

There is an expand/collapse button Right Blue Button available next to the “Number of matches”. When clicked, it shows the list of identical genes or proteins. The protein function and genome names are hyperlinked to feature and genome landing pages respectively for detailed information.