RE: [GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

So, The PlugIn which you are writing will not be taking care detail =
Prosite data, right?
If yes then I will write a separate plugin to load detail Prosite master =
data.

Thanks
Sanjeev

-----Original Message-----
From: Aaron J. Mackey [mailto:am...@pc...]
Sent: Tuesday, August 02, 2005 5:01 PM
To: Kumar, Sanjeev (Contr)
Cc: Jian Lu; gus...@li...
Subject: Re: [GUSDEV] Loading Prosite DB


Yes, InterProScan only provides domain analysis results, not the =20
actual domain/pattern/motif databases themselves.

-Aaron

On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote:

> Hi Aaron/Jian,
>    The Interproscan data has only PrositeID and description in it. =20
> But to load other information for a prosite ID, we need to load the =20
> Prosite data which comes in different format than Interpro.
> That is what I found, Do you copy?
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: Aaron J. Mackey [mailto:am...@pc...]
> Sent: Tuesday, August 02, 2005 4:43 PM
> To: Jian Lu
> Cc: Kumar, Sanjeev (Contr)
> Subject: Re: [GUSDEV] Loading Prosite DB
>
>
>
>  From http://www.ebi.ac.uk/interpro/README1.html
>
> PROSITE patterns.
>
> Some biologically significant amino acid patterns can be summarised
> in the form of regular expressions.
>
> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R.
> 1994) .
>
> PROSITE profile.
>
> There are a number of protein families as well as functional or
> structural domains that cannot be detected using patterns due to
> their extreme sequence divergence; the use of techniques based on
> weight matrices (also known as profiles) allows the detection of such
> domains.
>
>    pfscan from thePftools package (by Phi...@is...).
>
> PRINTS.
> The PRINTS database houses a collection of protein family
> fingerprints. These are groups of motifs that together are
> diagnostically more potent than single motifs by making use of the
> biological context inherent in a multiple-motif method.
>
>       FingerPRINTScan (Scordis, P. et al. 1999) .
>
>   PFAM.
> Pfam is a database of protein domain families. Pfam contains curated
> multiple sequence alignments for each family and corresponding
> profile hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package (by Sean Eddy,
> ed...@ge..., http://hmmer.wustl.edu),
> DeCypher=99 (TimeLogic) implementation of HMM search.
>
>   PRODOM.
> ProDom families are built by an automated process based on a
> recursive use ofPSI-BLAST homology searches.
>
>       BlastProDom.pl (by Florence Servant, fse...@to...)
> =96 a filter on top of theBlast package (Altschul, S. F. et al. 1997) =
.
>
>   SMART.
> SMART domains are extensively annotated with respect to phyletic
> distributions, functional class, tertiary structures and functionally
> important residues. SMART alignments are optimised manually and
> following construction of corresponding hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package.
>
> TIGRFAMs.
> TIGRFAMs are a collection of protein families featuring curated
> multiple sequence alignments, Hidden Markov Models (HMMs) and
> associated information designed to support the automated functional
> identification of proteins by sequence homology. Classification by
> equivalog family (see below), where achievable, complements
> classification by orthologs, superfamily, domain or motif. It
> provides the information best suited for automatic assignment of
> specific functions to proteins from large scale genome sequencing
> projects
>
> =D8     hmmpfam from theHMMER2.1 package.
>
> Optionally, predictions for coiled-coil, signal peptide cleavage
> sites (SignalP v2) and TM helices (TMHMM v2) are supported.
>
>
>
> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote:
>
>
>> I don't think so. Here is the data sheet from InterProScan.
>>
>> Kumar, Sanjeev (Contr) wrote:
>>
>>
>>
>>> Hi Aaron/Jian,
>>>   What all types of data we are talking in IterProScan plugin?
>>>  Does it include Prosite data.
>>> Thanks
>>> Sanjeev
>>>
>>> -----Original Message-----
>>> From: Jian Lu [mailto:jl...@vb...]
>>> Sent: Tuesday, August 02, 2005 2:02 PM
>>> To: Aaron J. Mackey
>>> Cc: Kumar, Sanjeev (Contr); gus...@li...
>>> Subject: Re: [GUSDEV] Loading Prosite DB
>>>
>>>
>>> Aaron,
>>>
>>> We are also working on InterProScan and other analysis tools. But
>>> we haven't got a plugin yet. If your plugin is ready, I would like
>>> to play it. Here is the view that we created for InterProScan.
>>> Please comment it. Thanks.
>>>
>>> --
>>> -- VIEW DOTS.INTERPROSCAN
>>> -- used to store outputs from InterProScan
>>> -- June 29, 2005
>>>
>>>
>>>
>>
>>
>> <InterProScan_OUTPUT.pdf>
>>
>>
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017