Re: [Gusdev-gusdev] LoadBlastSimFast plugin

[Sucheta T. <su...@vb...>]

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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