Locus Details

This page displays details about a single locus. It also contains a button back 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.

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Figure 1.1: Locus Details page.

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).

../_images/locus_details_hist.png

Figure 2.1: Number of alleles (744) that have a length in the range of 5595-5599 (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.

../_images/locus_details_scatter.png

Figure 3.1: Length (5232 bp) of allele 1677.

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.

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Figure 4.1: Locus Details table.

Interactive Buttons

Below the Locus Details table, there are 3 buttons 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.

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In this case you should download the fasta file with the allele sequences and perform the query using your favorite interface.