{% extends "base.html" %} {% set active_page = "description-extractor" %} {% set page_title = "Variant Description Extractor" %} {% block content %}

Please note that this is an experimental service and we are currently limiting input sequences to {{ '{:,}'.format(extractor_max_input_length) }} bp.

Extract the HGVS variant description from a reference sequence and an observed sequence. For now, we require the user to fill in two sequences. After the testing phase, we plan to use the underlying algorithm for:

The algorithm is implemented in the HGVS variant description extractor. To apply it on longer input sequences than accepted on this page, you can download that package and run it locally.

Please supply a reference sequence and an observed sequence.

Reference input

Example: ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA

Example: NM_004006.1

Sample input

Example: ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA

Example: NM_004006.2

Help
{% if reference_method and sample_method %}
{% for m in messages %} {% if m.class == "error" %}

{{ m.description }}

{% elif m.class == "warning" %}

{{ m.description }}

{% elif m.class == "information" %}

{{ m.description }}

{% elif m.class == "debug" %}

{{ m.description }}

{% endif %} {% endfor %} {% if summary == "0 Errors, 0 Warnings." %}

{{ summary }}

{% else %}

{{summary}}

{% endif %} {% if not errors %}

Input

Field Value
Reference input {% if reference_method == 'raw_method' %} {{ reference_sequence|short(40) }} {% elif reference_method == 'file_method' %} {{ reference_filename|default('File upload', true) }} {% elif reference_method == 'refseq_method' %} {{ reference_accession_number }} {% endif %}
Sample input {% if sample_method == 'raw_method' %} {{ sample_sequence|short(40) }} {% elif sample_method == 'file_method' %} {{ sample_filename|default('File upload', true) }} {% elif sample_method == 'refseq_method' %} {{ sample_accession_number }} {% endif %}

Description

{{ raw_vars|string }}

Overview of the raw variants

{% for raw_var in raw_vars %} {% endfor %}
Start End Type Deleted Inserted Shift Description
{{ raw_var.start }} {{ raw_var.end }} {{ raw_var.type }} {{ raw_var.deleted|string|short }} {{ raw_var.inserted|string|short }} {{ raw_var.shift }} {% if raw_var|string|length > 20 %}Too long to show{% else %}{{ raw_var|string }}{% endif %}

Please note that the generated descriptions use one-based coordinates where we start counting at the start of the supplied sequence. This means that for genomic reference sequences, the result will be in g. coordinates, while for transcripts the result will be in n. coordinates.

{% endif %}{# not errors #} {% endif %}{# description #} {% endblock content %}