Re: [GUSDEV] LoadBLATAlignment and gaptables

[Y. T. G. <yon...@pc...>]

Yes you should use the new version from now on, but if you have already 
loaded all your alignments then there is no reason for a redo.

The plugin reads the raw output files (.pls files) from the BLAT program 
that you ran prior to your calling this plugin, so if you do not delete 
those files, the original alignment results will be there. There are 
several rounds of filtering:
1) the BLAT program by default only reports DNA alignments of 
identity >= 90% and alignment score of >= 30 (i.e. roughly 30 nucleotides in length). 
Alignments inferior in quality will not be in you .pls files
2) the LoadBLATAlignments plugin by default (you can certainly adjust 
this) discards alignments that span less than 10% of the query. These 
alignments will stay in the raw output files but they won't be loaded into 
GUS. Whether an alignment is loaded is not affected in anyway by the 4 
categories: they are just there as an annotation.
3) the plugin also has a "keep_best" option. If it is set to 1, it keeps 
the best alignment for each query sequence while deleting others. If it is 
set to 2, it keeps top alignments (whoses alignment score is within 1% of 
the best score, defined as the square root of %identity times %query 
aligned, for that specific query sequence).

Hope this helps and let me know if you have more questions.

-Thomas

On Sun, 1 May 2005, Sucheta Tripathy wrote:

> Hi Thomas,
>
> Thanks for the reply. I am using the older version of the plugin, I will
> update it..
>
> In fact, now I forced the alignments to be loaded even without the
> gaptables, by assigning some return values in BLAT::Alignment file. I
> guess it is not the right way to do.
>
> Another question I have is, with the new plugin, is there a possibility
> that some of the alignments will be thrown out, if it does not belong to
> these 4 categories? In this particular instance I found atleast some of
> the alignments are thrown out, and also if the alignments that are not
> loaded, are they stored in some file for look up later.
>
> Many thanks
>
> Sucheta
>> Hi Sucheta:
>> What version of the plugin are you using? The latest version (1.35) has
>> gapTableSpace as a command line option, and it is optional.
>>
>> When we load BLAT alignments of cDNAs, we may take into consideration
>> alignments that span or fall on the edge of a gap in the genomic sequence.
>> We usually import the per chromosome gap tables from GoldenPath into a
>> temporary table space. The temp table space (e.g. ygan is my personal
>> schema) needs to be separate from GUS schemas as DDL operations to them
>> are restricted and the number and names of gap tables change from version
>> to version. The gap information is only used to classify alignments into
>> one of 4 categories: very good alignments, very good but contain/close to
>> genomic gaps, good, and others.
>>
>> That said, you may not care about gaps at all or can safely ignore
>> the impact of gaps in your case. As of a version later than the one you
>> have, you do not have to worry about gap tables any more - just do not
>> set the gapTableSpace option in the command line.
>>
>> -Thomas
>>
>> On Fri, 29 Apr 2005, Sucheta Tripathy wrote:
>>
>>> Dear group,
>>>
>>> I am trying to use the plugin LoadBLATAlignment, but can't figure out
>>> where
>>> to define my gaptable(as I see in line 452
>>>
>>> 452     my $gapTable = 'ygan.' . $ext_genome_ver . '_' . $target_id .
>>> '_gap'
>>>    ;)
>>>
>>> If I have to define a table for gap regions, can anyone please suggest
>>> what
>>> are the fields.
>>>
>>> Do I need to pre-load some data into them?
>>>
>>> Many thanks
>>>
>>> Sucheta
>>>
>>>
>>>
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>
>
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>
>
>
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