Re: [MUMmer-help] show-diff documentation?

[Adam P. <aph...@gm...>]

Timothy,
The GAP feature annotates two adjacent, and possibly, overlapping
alignments. If the difference is negative on the reference, the alignments
overlap on the reference. If the difference is negative on the query, the
alignments overlap on the query. Overlapping alignments are a sign of
duplications. See the attached reference, which may make things clearer.
When the alignments overlap in both the reference and query, it's a tandem
expansion/collapse event (e.g. ARRB -> ARRRB in the examples).

DUP features are for when the duplicated sequence is contained in its own
separate alignment. Examples of this type would be the "Collapse w/
Insertion" alignments shown in the attachment (ARB -> ARIRB in the
examples).

BRK is when the beginning or end of a query sequence doesn't map to the
reference. All the other features report a junction between two adjacent
alignments. BRK reports the case of an alignment not extending all the way
to the beginning or end of a sequence.

Hope this helps,
-Adam


On Thu, Feb 12, 2015 at 11:34 PM, Timothy Wu <2h...@gm...> wrote:

> Hi,
>
> Could someone help me with this question I posted at BioStar?
>
> Thanks.
>
> https://www.biostars.org/p/130363/
>
> Timothy
>
>
>
>
> On Thu, Dec 11, 2014 at 3:24 PM, Timothy Wu <2h...@gm...> wrote:
>
>> Dear Adam,
>>
>> Yes that was indeed me. That email account is not stable as of lately.
>> I've been missing many emails from many people. Thanks for your help I
>> appreciate it. That top-level README is easy to miss but definitely more
>> descriptive.
>>
>> Everything else is clear, however, I am not sure about GAP.
>>
>> "gap-length-R is the length of the alignment gap in the reference". I
>> don't understand when itself (or gap-legnth-Q for that matter) is negative,
>> where gap_end - gap_start is negative. (Why is the coordinates for end
>> smaller than start?) Hence I don't follow where it says "If gap-diff is
>> positive, sequence has been inserted in the reference", and the rest of the
>> explanations.
>>
>> GAP is suppose to be different from BRK or DUP, why is it talking about
>> tandem duplications, and not label it as DUP? (BTW what does BRK stands
>> for?)
>>
>> Thanks for your help. :)
>>
>> Timothy
>>
>>
>>
>> Timothy
>>
>>
>> On Fri, Nov 21, 2014 at 12:45 AM, Adam Phillippy <aph...@gm...>
>> wrote:
>>
>>> Timothy,
>>> The documentation for show-diff is in the top-level README (in
>>> MUMmer/README). I also believe I responded with additional information to
>>> an email you sent directly to me yesterday. (or at least to someone who
>>> happens to have your same name!)
>>>
>>> Best,
>>> -Adam
>>>
>>>
>>> On Wed, Nov 19, 2014 at 9:35 PM, Timothy Wu <2h...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I would like to know if there is any documentation for show-diff. I
>>>> find it difficult to understand. The documentation to dnadiff told us to
>>>> see documentation for various tools, but I can't find any doc for
>>>> show-diff. I've read the stuff with the -h flag but I still find it hard to
>>>> digest. Any help appreciated, thanks.
>>>>
>>>> Timothy
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>>>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>>>> with Interactivity, Sharing, Native Excel Exports, App Integration &
>>>> more
>>>> Get technology previously reserved for billion-dollar corporations, FREE
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> MUMmer-help mailing list
>>>> MUM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>>
>>>>
>>>
>>
>