Locus Details
This page displays details about a single locus. It also contains a button to return to the Schemas page.
Note
The Locus Details panel is by default expanded. It can be collapsed by clicking on the arrow icon on the upper-right corner of the panel.
Histogram
The histogram represents the number of alelles (y-axis) having a length within a given range (x-axis).
For example, Figure 2 shows that 744 alleles of locus INNUENDO_cgMLST-016801 vary in length between 5595 and 5599 base pairs (bp).
Scatter
The scatterplot represents the sequence size in base pairs (y-axis) of each allele (x-axis) of the locus.
For example, Figure 3 shows that allele 1877 of locus INNUENDO_cgMLST-016801 has a length of of 5232 base pairs.
Details table
The locus details table displays the following information about the locus:
Locus Label: the Chewie-NS label assigned to the locus.
Number of Alleles: the total number of alleles of the locus.
Size Range (bp): the range of sequence lengths of the alleles in base pairs.
Median Size: the median of the allele lengths in base pairs.
Uniprot Label: the Uniprot annotation.
Uniprot URI: the URI of the Uniprot annotation. Clicking on the URI will open the page of the Uniprot annotation.
Interactive Buttons
Below the Locus Details table, there are 3 buttons allowing the following operations:
Download FASTA: downloads a FASTA file of the locus.
BLASTX: opens a BLASTX webpage with the sequence of allele 1 already introduced in the search box.
BLASTN: opens a BLASTN webpage with the sequence of allele 1 already introduced in the search box.
Note
The BLAST search will only occur if the first allele of the selected locus has a sequence length < 8000 bps. If an allele has more than 8000 bps, the following warning will appear.
In this case you should download the fasta file with the allele sequences and perform the query using your favorite interface.