Re: [Gusdev-gusdev] LoadBlastSimFast plugin

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sucheta-

the way we use the similarity table is between sequences that are in the 
database.   the query is, for example, an Allgenes or PlasmoDB gene.    
And, yes, we load NRDB, which is the target.  

it all depends on what you plan on doing with your blast results.   but, 
our standard model is that the blast results are information most 
importantly associated with a gene that we care about.   so, you get to 
the blast results from the gene by the similarity table.

if you have the target sequence in the db, then you can show the user 
the definition line of the target and the sequence.

so, the LoadBlastSimFast plugin works is that it assumes the query and 
target sequences have previously been loaded, and it is just 
establishing a similarity relationship between them

steve

Sucheta Tripathy wrote:

> Steve,
>
> I have the outputs generated from blast results after blasting against 
> several databases(Like NR, Several different organisms), so Do I need 
> to put the subject sequences in some of the GUS tables? If so where?
>
> Similarly, for the querytable, do I have to put the query sequences 
> first into NAsequenceImp tables?
>
> I am not quite sure, if I understood the concept correctly. When I 
> upload blast results to some database, I parse them and store them 
> into some tables with the HSP regions, which I don't see in the parsed 
> output? Is it why you want the querytable and subjecttable to have the 
> sequences stored?
>
> Can you please send me some example?
>
> Thanks
>
> Sucheta
>
> At 06:49 PM 7/6/2004 -0400, Steve Fischer wrote:
>
>> Sucheta-
>>
>> At first glance, the output looks ok, so let's assume Michael's 
>> script works.
>>
>> similarities are between two things, the query (your sequence) and 
>> the subject (the sequences you are blasting against).
>>
>> the querytable is the table that holds the sequences you are blasting.
>>
>> the subjecttable is the table that holds the sequences you are 
>> blasting against.
>>
>> --file is the arg that you pass the file to.
>>
>> hope that helps,
>> steve
>>
>> Sucheta Tripathy wrote:
>>
>>> I am trying to load a bunch of blast output files using the 
>>> LoadBlastSimFast plugin. First I have parsed the blast output with a 
>>> script 'ParseFileForSimilarity.pl' I obtained from Michael. As I see 
>>> from the plugin comments, the blast output need to be parsed by a 
>>> script
>>> 'generateBlastSimilarity.pl'. I am not sure if both the parsing 
>>> scripts do the same job..
>>>
>>> I am not sure for the LoadBlastSimFast plugin what value should I 
>>> pass for --QueryTable and --SubjectTable and
>>> Which parameter takes the parsed blast output file.
>>>
>>> My blast output is currently formatted into the following fileds 
>>> using ParseFileForSimilarity:
>>>
>>> Cutoff parameters:
>>>         P value: 1e-05
>>>         Length:
>>> 10
>>>         Percent Identity: 20
>>>
>>> >CL1Contig2 (35 subjects)
>>>   Sum: AAA83776.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3
>>>    HSP1: AAA83776.1:54:63:83:99:6e-20:54:133:30:278:0:+3
>>>   Sum: XP_342001.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3
>>>    HSP1: XP_342001.1:54:63:83:99:6e-20:54:133:30:278:0:+3
>>>   Sum: AAB52915.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3
>>>    HSP1: AAB52915.1:54:63:83:99:6e-20:54:133:30:278:0:+3
>>>   Sum: NP_032016.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3
>>>    HSP1: NP_032016.1:54:63:83:99:6e-20:54:133:30:278:0:+3
>>>   Sum: NP_001988.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3
>>>    HSP1: NP_001988.1:54:63:83:99:6e-20:54:133:30:278:0:+3
>>>   Sum: XP_345683.1:99:6e-20:72:151:30:278:1:83:54:63:0:+3
>>>    HSP1: XP_345683.1:54:63:83:99:6e-20:72:151:30:278:0:+3
>>>   Sum: BAB68608.1:99:6e-20:58:137:30:278:1:83:54:63:0:+3
>>>    HSP1: BAB68608.1:54:63:83:99:6e-20:58:137:30:278:0:+3
>>>   Sum: NP_777156.1:97:2e-19:54:133:30:278:1:83:53:63:0:+3
>>>    HSP1: NP_777156.1:53:63:83:97:2e-19:54:133:30:278:0:+3
>>>   Sum: NP_598374.1:97:2e-19:54:132:30:275:1:82:53:62:0:+3
>>>    HSP1: NP_598374.1:53:62:82:97:2e-19:54:132:30:275:0:+3
>>>   Sum: AAQ63318.1:96:3e-19:53:133:27:278:1:84:54:64:0:+3
>>>    HSP1: AAQ63318.1:54:64:84:96:3e-19:53:133:27:278:0:+3
>>>   Sum: BAB68610.1:96:4e-19:58:137:30:278:1:83:53:62:0:+3
>>>    HSP1: BAB68610.1:53:62:83:96:4e-19:58:137:30:278:0:+3
>>>   Sum: AAK95215.1:93:3e-18:54:133:30:278:1:83:54:60:0:+3
>>>    HSP1: AAK95215.1:54:60:83:93:3e-18:54:133:30:278:0:+3
>>>   Sum: AAN05597.1:90:2e-17:51:131:27:278:1:84:52:61:0:+3
>>>    HSP1: AAN05597.1:52:61:84:90:2e-17:51:131:27:278:0:+3
>>>   Sum: NP_505007.1:90:2e-17:51:130:30:278:1:83:51:62:0:+3
>>>    HSP1: NP_505007.1:51:62:83:90:2e-17:51:130:30:278:0:+3
>>>   Sum: AAL49305.2:90:3e-17:86:146:90:278:1:63:47:52:0:+3
>>>    HSP1: AAL49305.2:47:52:63:90:3e-17:86:146:90:278:0:+3
>>>   Sum: NP_650922.1:90:3e-17:71:131:90:278:1:63:47:52:0:+3
>>>    HSP1: NP_650922.1:47:52:63:90:3e-17:71:131:90:278:0:+3
>>>   Sum: AAK92197.1:89:6e-17:71:131:90:278:1:63:47:52:0:+3
>>>    HSP1: AAK92197.1:47:52:63:89:6e-17:71:131:90:278:0:+3
>>>   Sum: XP_343942.1:86:3e-16:68:144:30:278:1:83:50:58:0:+3
>>>    HSP1: XP_343942.1:50:58:83:86:3e-16:68:144:30:278:0:+3
>>>   Sum: Q05472:86:4e-16:1:59:96:278:1:61:46:50:0:+3
>>>    HSP1: Q05472:46:50:61:86:4e-16:1:59:96:278:0:+3
>>>   Sum: XP_311180.1:85:7e-16:61:139:42:281:1:81:48:60:0:+3
>>>    HSP1: XP_311180.1:48:60:81:85:7e-16:61:139:42:281:0:+3
>>>   Sum: CAC86461.1:84:2e-15:2:61:93:278:1:62:46:51:0:+3
>>>    HSP1: CAC86461.1:46:51:62:84:2e-15:2:61:93:278:0:+3
>>>   Sum: NP_473105.1:81:9e-15:2:58:93:278:1:62:45:47:0:+3
>>>    HSP1: NP_473105.1:45:47:62:81:9e-15:2:58:93:278:0:+3
>>>   Sum: NP_194668.1:80:2e-14:2:66:93:275:2:122:88:94:0:+3
>>>    HSP1: NP_194668.1:44:47:61:80:2e-14:2:60:93:275:0:+3
>>>    HSP2: NP_194668.1:44:47:61:80:2e-14:8:66:93:275:0:+3
>>>   Sum: CAD98413.1:80:3e-14:3:58:96:272:1:59:44:47:0:+3
>>>    HSP1: CAD98413.1:44:47:59:80:3e-14:3:58:96:272:0:+3
>>>   Sum: O22424:80:3e-14:1:259:195:971:1:259:169:209:1:-1
>>>    HSP1: O22424:169:209:259:80:3e-14:1:259:195:971:1:-1
>>>   Sum: P47961:80:3e-14:1:253:213:971:1:253:164:204:1:-1
>>>
>>> Thanks
>>>
>>> Sucheta
>>>
>>>
>>>
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>>
>>
>>
>>
>>
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