.. _allele_differences:

********************************
Investigating allele differences
********************************

.. index::
   single: sequence similarity; determining

Sequence similarity
===================
To find sequences most similar to a selected allele within a sequence 
definition database, expand the 'Analysis' menu item and click 
'Sequence similarity' on the contents page.

.. image:: /images/data_query/sequence_similarity.png

Enter the locus and allele identifer of the sequence to investigate and the 
number of nearest matches you'd like to see, then press submit.

.. image:: /images/data_query/sequence_similarity2.png

A list of nearest alleles will be displayed, along with the percentage identity
and number of gaps between the sequences.

.. image:: /images/data_query/sequence_similarity3.png

Click the appropriate 'Compare' button to display a list of nucleotide 
differences and/or a sequence alignment.

.. image:: /images/data_query/sequence_similarity4.png

Sequence comparison
===================
To directly compare two sequences, expand the 'Analysis' section and click 
'Sequence comparison' on the contents page of a sequence definition database.

.. image:: /images/data_query/sequence_comparison.png

Enter the locus and two allele identifiers to compare.  Press submit.

.. image:: /images/data_query/sequence_comparison2.png

A list of nucleotide differences and/or an alignment will be displayed.

.. image:: /images/data_query/sequence_comparison3.png

.. seealso::

   :ref:`Locus explorer plugin <locus_explorer>`.