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Loculus bot committed Jul 4, 2024
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145 changes: 78 additions & 67 deletions website/src/components/SearchPage/DisplaySearchDocs.tsx
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Expand Up @@ -48,81 +48,92 @@ const DisplaySearchDocs: React.FC = () => {
<X className='h-6 w-6' />
</button>
<h3 className='font-bold text-2xl mb-4 text-primary-700'>Mutation Search</h3>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Nucleotide Mutations and Insertions</h4>
<p className='mb-2'>
For a single-segmented organism, nucleotide mutations have the format{' '}
<b>&lt;position&gt;&lt;base&gt;</b> or <b>&lt;base_ref&gt;&lt;position&gt;&lt;base&gt;</b>.
A <b>&lt;base&gt;</b> can be one of the four nucleotides <b>A</b>, <b>T</b>, <b>C</b>, and{' '}
<b>G</b>. It can also be <b>-</b> for deletion and <b>N</b> for unknown. For example if the
reference sequence is <b>A</b> at position <b>23</b> both: <b>23T</b> and <b>A23T</b> will
yield the same results.
</p>
<p className='mb-2'>
If your organism is multi-segmented you must append the name of the segment to the start of
the mutation, e.g. <b>S:23T</b> and <b>S:A23T</b> for a mutation in segment <b>S</b>.
</p>
<p className='mb-2'>
Insertions can be searched for in the same manner, they just need to have <b>ins_</b>{' '}
appended to the start of the mutation. Example <b>ins_10462:A</b> or if the organism is
multi-segmented <b>ins_S:10462:A</b>.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>
Nucleotide Mutations and Insertions
</h4>
<p className='mb-2'>
For a single-segmented organism, nucleotide mutations have the format{' '}
<b>&lt;position&gt;&lt;base&gt;</b> or{' '}
<b>&lt;base_ref&gt;&lt;position&gt;&lt;base&gt;</b>. A <b>&lt;base&gt;</b>{' '}
can be one of the four nucleotides <b>A</b>, <b>T</b>, <b>C</b>, and{' '}
<b>G</b>. It can also be <b>-</b> for deletion and <b>N</b> for unknown. For
example if the reference sequence is <b>A</b> at position <b>23</b> both:{' '}
<b>23T</b> and <b>A23T</b> will yield the same results.
</p>
<p className='mb-2'>
If your organism is multi-segmented you must append the name of the segment
to the start of the mutation, e.g. <b>S:23T</b> and <b>S:A23T</b> for a
mutation in segment <b>S</b>.
</p>
<p className='mb-2'>
Insertions can be searched for in the same manner, they just need to have{' '}
<b>ins_</b> appended to the start of the mutation. Example{' '}
<b>ins_10462:A</b> or if the organism is multi-segmented{' '}
<b>ins_S:10462:A</b>.
</p>
</div>

<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Amino Acid Mutations and Insertions</h4>
<p className='mb-2'>
An amino acid mutation has the format <b>&lt;gene&gt;:&lt;position&gt;&lt;base&gt;</b> or{' '}
<b>&lt;gene&gt;:&lt;base_ref&gt;&lt;position&gt;&lt;base&gt;</b>. A <b>&lt;base&gt;</b> can
be one of the 20 amino acid codes. It can also be <b>-</b> for deletion and <b>X</b> for
unknown. Example: <b>E:57Q</b>.
</p>
<p className='mb-2'>
Insertions can be searched for in the same manner, they just need to have <b>ins_ </b>
appended to the start of the mutation. Example <b>ins_NS4B:31:N</b>.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>
Amino Acid Mutations and Insertions
</h4>
<p className='mb-2'>
An amino acid mutation has the format{' '}
<b>&lt;gene&gt;:&lt;position&gt;&lt;base&gt;</b> or{' '}
<b>&lt;gene&gt;:&lt;base_ref&gt;&lt;position&gt;&lt;base&gt;</b>. A{' '}
<b>&lt;base&gt;</b> can be one of the 20 amino acid codes. It can also be{' '}
<b>-</b> for deletion and <b>X</b> for unknown. Example: <b>E:57Q</b>.
</p>
<p className='mb-2'>
Insertions can be searched for in the same manner, they just need to have{' '}
<b>ins_ </b>
appended to the start of the mutation. Example <b>ins_NS4B:31:N</b>.
</p>
</div>

<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Insertion Wildcards</h4>
<p className='mb-2'>
Loculus supports insertion queries that contain wildcards <b>?</b>. For example{' '}
<b>ins_S:214:?EP?</b> will match all cases where segment <b>S</b> has an insertion of{' '}
<b>EP</b> between the positions 214 and 215 but also an insertion of other AAs which include
the <b>EP</b>, e.g. the insertion <b>EPE</b> will be matched.
</p>
<p className='mb-2'>
You can also use wildcards to match any insertion at a given position. For example{' '}
<b>ins_S:214:?:</b> will match any (but at least one) insertion between the positions 214
and 215.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Insertion Wildcards</h4>
<p className='mb-2'>
Loculus supports insertion queries that contain wildcards <b>?</b>. For
example <b>ins_S:214:?EP?</b> will match all cases where segment <b>S</b>{' '}
has an insertion of <b>EP</b> between the positions 214 and 215 but also an
insertion of other AAs which include the <b>EP</b>, e.g. the insertion{' '}
<b>EPE</b> will be matched.
</p>
<p className='mb-2'>
You can also use wildcards to match any insertion at a given position. For
example <b>ins_S:214:?:</b> will match any (but at least one) insertion
between the positions 214 and 215.
</p>
</div>

<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Multiple Mutations</h4>
<p className='mb-2'>
Multiple mutation filters can be provided by adding one mutation after the other.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Multiple Mutations</h4>
<p className='mb-2'>
Multiple mutation filters can be provided by adding one mutation after the
other.
</p>
</div>

<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Any Mutation</h4>
<p className='mb-2'>
To filter for any mutation at a given position you can omit the <b>&lt;base&gt;</b>.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>No Mutation</h4>
<p className='mb-2'>
You can write a <b>.</b> for the <b>&lt;base&gt;</b> to filter for sequences for which it is
confirmed that no mutation occurred, i.e. has the same base as the reference genome at the
specified position.
</p>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>Any Mutation</h4>
<p className='mb-2'>
To filter for any mutation at a given position you can omit the{' '}
<b>&lt;base&gt;</b>.
</p>
</div>
<div className='mb-4'>
<h4 className='font-bold text-l mb-4 text-primary-700'>No Mutation</h4>
<p className='mb-2'>
You can write a <b>.</b> for the <b>&lt;base&gt;</b> to filter for sequences
for which it is confirmed that no mutation occurred, i.e. has the same base
as the reference genome at the specified position.
</p>
</div>
</DialogPanel>
</Transition.Child>
</div>

</div>
</Dialog>
</Transition>
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