RE: [GUSDEV] RE: Gusdev-gusdev digest, Vol 1 #637 - 1 msg

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

Hi Chris,
   Here is the sample example,
   It doesn't have any sequence.=20

ID   ASX_HYDROXYL; PATTERN.
AC   PS00010;
DT   APR-1990 (CREATED); APR-1990 (DATA UPDATE); APR-2005 (INFO UPDATE).
DE   Aspartic acid and asparagine hydroxylation site.
PA   C-x-[DN]-x(4)-[FY]-x-C-x-C.
NR   /RELEASE=3D46.6,180652;
NR   /TOTAL=3D1358(269); /POSITIVE=3D1342(260); /UNKNOWN=3D0(0); =
/FALSE_POS=3D16(9);
NR   /FALSE_NEG=3D0; /PARTIAL=3D0;
CC   /TAXO-RANGE=3D??E??; /MAX-REPEAT=3D43;
CC   /SITE=3D3,hydroxylation;
CC   /VERSION=3D1;
DR   P31696, AGRN_CHICK , T; Q90404, AGRN_DISOM , T; P13497, BMP1_HUMAN =
, T;
DR   P98063, BMP1_MOUSE , T; P98070, BMP1_XENLA , T; P98069, BMPH_STRPU =
, T;
DR   Q9NPY3, C1QR1_HUMAN, T; O89103, C1QR1_MOUSE, T; Q9ET61, C1QR1_RAT  =
, T;
DR   P00736, C1R_HUMAN  , T; Q8CG16, C1R_MOUSE  , T; Q5R1W3, C1R_PANTR  =
, T;
DR   P09871, C1S_HUMAN  , T; P15156, CASP_MESAU , T; Q8SQA4, CD97_BOVIN =
, T;
DR   P48960, CD97_HUMAN , T; Q9Z0M6, CD97_MOUSE , T; Q9NYQ6, =
CELR1_HUMAN, T;
DR   O35161, CELR1_MOUSE, T; Q9HCU4, CELR2_HUMAN, T; Q9R0M0, =
CELR2_MOUSE, T;
DR   Q9QYP2, CELR2_RAT  , T; Q9NYQ7, CELR3_HUMAN, T; Q91ZI0, =
CELR3_MOUSE, T;
DR   O88278, CELR3_RAT  , T; Q86T13, CN027_HUMAN, T; Q8VCP9, =
CN027_MOUSE, T;
DR   P10040, CRB_DROME  , T; P82279, CRUM1_HUMAN, T; P81282, =
CSPG2_BOVIN, T;
DR   Q90953, CSPG2_CHICK, T; P13611, CSPG2_HUMAN, T; Q28858, =
CSPG2_MACNE, T;
DR   Q62059, CSPG2_MOUSE, T; Q9ERB4, CSPG2_RAT  , T; O14594, =
CSPG3_HUMAN, T;
DR   P55066, CSPG3_MOUSE, T; Q5IS41, CSPG3_PANTR, T; P55067, CSPG3_RAT  =
, T;
DR   P80370, DLK_HUMAN  , T; Q09163, DLK_MOUSE  , T; O00548, DLL1_HUMAN =
, T;
DR   Q61483, DLL1_MOUSE , T; P97677, DLL1_RAT   , T; Q9NR61, DLL4_HUMAN =
, T;
DR   Q9JI71, DLL4_MOUSE , T; P10041, DL_DROME   , T; O43854, =
EDIL3_HUMAN, T;
DR   O35474, EDIL3_MOUSE, T; O75095, EGFL3_HUMAN, T; O88281, EGFL3_RAT  =
, T;
DR   Q7Z7M0, EGFL4_HUMAN, T; P60882, EGFL4_MOUSE, T; Q9QYP0, EGFL4_RAT  =
, T;
DR   Q9UHF1, EGFL7_HUMAN, T; Q6AZ60, EGFL7_RAT  , T; Q99944, =
EGFL8_HUMAN, T;
DR   Q6GUQ1, EGFL8_MOUSE, T; Q6MG84, EGFL8_RAT  , T; Q6UY11, =
EGFL9_HUMAN, T;
DR   Q8K1E3, EGFL9_MOUSE, T; Q9BEA0, EGF_CANFA  , T; Q95ND4, EGF_FELCA  =
, T;
DR   P01133, EGF_HUMAN  , T; P01132, EGF_MOUSE  , T; Q00968, EGF_PIG    =
, T;
DR   P07522, EGF_RAT    , T; Q9HBW9, ELTD1_HUMAN, T; Q923X1, =
ELTD1_MOUSE, T;
DR   Q9ESC1, ELTD1_RAT  , T; Q14246, EMR1_HUMAN , T; Q61549, EMR1_MOUSE =
, T;
DR   Q9UHX3, EMR2_HUMAN , T; Q9BY15, EMR3_HUMAN , T; Q86SQ3, EMR4_HUMAN =
, T;
DR   Q91ZE5, EMR4_MOUSE , T; P00743, FA10_BOVIN , T; P25155, FA10_CHICK =
, T;
DR   P83370, FA10_HOPST , T; P00742, FA10_HUMAN , T; O88947, FA10_MOUSE =
, T;
DR   O19045, FA10_RABIT , T; Q63207, FA10_RAT   , T; P81428, FA10_TROCA =
, T;
DR   P22457, FA7_BOVIN  , T; P08709, FA7_HUMAN  , T; P70375, FA7_MOUSE  =
, T;
DR   P98139, FA7_RABIT  , T; Q8K3U6, FA7_RAT    , T; P00741, FA9_BOVIN  =
, T;
DR   P19540, FA9_CANFA  , T; Q804X6, FA9_CHICK  , T; Q6SA95, FA9_FELCA  =
, T;
DR   P00740, FA9_HUMAN  , T; P16294, FA9_MOUSE  , T; Q95ND7, FA9_PANTR  =
, T;
DR   P16293, FA9_PIG    , T; Q9VW71, FAT2_DROME , T; Q14517, FATH_HUMAN =
, T;
DR   O42182, FBLN1_BRARE, T; O77469, FBLN1_CAEEL, T; Q8MJJ9, =
FBLN1_CERAE, T;
DR   O73775, FBLN1_CHICK, T; P23142, FBLN1_HUMAN, T; Q08879, =
FBLN1_MOUSE, T;
DR   P98095, FBLN2_HUMAN, T; P37889, FBLN2_MOUSE, T; Q12805, =
FBLN3_HUMAN, T;
DR   Q7YQD7, FBLN3_MACFA, T; Q8BPB5, FBLN3_MOUSE, T; O35568, FBLN3_RAT  =
, T;
DR   O55058, FBLN4_CRIGR, T; O95967, FBLN4_HUMAN, T; Q9WVJ9, =
FBLN4_MOUSE, T;
DR   Q9UBX5, FBLN5_HUMAN, T; Q9WVH9, FBLN5_MOUSE, T; Q9WVH8, FBLN5_RAT  =
, T;
DR   P98133, FBN1_BOVIN , T; P35555, FBN1_HUMAN , T; Q61554, FBN1_MOUSE =
, T;
DR   Q9TV36, FBN1_PIG   , T; P35556, FBN2_HUMAN , T; Q61555, FBN2_MOUSE =
, T;
DR   Q75N90, FBN3_HUMAN , T; P10079, FBP1_STRPU , T; P49013, FBP3_STRPU =
, T;
DR   Q25464, FP2_MYTGA  , T; Q14393, GAS6_HUMAN , T; Q61592, GAS6_MOUSE =
, T;
DR   Q63772, GAS6_RAT   , T; P13508, GLP1_CAEEL , T; Q90Y57, =
JAG1A_BRARE, T;
DR   Q90Y54, JAG1B_BRARE, T; P78504, JAG1_HUMAN , T; Q9QXX0, JAG1_MOUSE =
, T;
DR   Q63722, JAG1_RAT   , T; Q9Y219, JAG2_HUMAN , T; Q9QYE5, JAG2_MOUSE =
, T;
DR   P97607, JAG2_RAT   , T; Q99087, LDLR1_XENLA, T; Q99088, =
LDLR2_XENLA, T;
DR   P35950, LDLR_CRIGR , T; P01130, LDLR_HUMAN , T; P35951, LDLR_MOUSE =
, T;
DR   Q28832, LDLR_PIG   , T; P20063, LDLR_RABIT , T; P35952, LDLR_RAT   =
, T;
DR   P14585, LIN12_CAEEL, T; Q9NZR2, LRP1B_HUMAN, T; Q9JI18, =
LRP1B_MOUSE, T;
DR   P98157, LRP1_CHICK , T; Q07954, LRP1_HUMAN , T; P98164, LRP2_HUMAN =
, T;
DR   P98158, LRP2_RAT   , T; O75096, LRP4_HUMAN , T; Q8VI56, LRP4_MOUSE =
, T;
DR   Q9QYP1, LRP4_RAT   , T; Q98931, LRP8_CHICK , T; Q14114, LRP8_HUMAN =
, T;
DR   Q924X6, LRP8_MOUSE , T; Q04833, LRP_CAEEL  , T; Q14766, =
LTB1L_HUMAN, T;
DR   Q8CG19, LTB1L_MOUSE, T; P22064, LTB1S_HUMAN, T; Q8CG18, =
LTB1S_MOUSE, T;
DR   Q00918, LTBP1_RAT  , T; Q28019, LTBP2_BOVIN, T; Q14767, =
LTBP2_HUMAN, T;
DR   O08999, LTBP2_MOUSE, T; O35806, LTBP2_RAT  , T; Q9NS15, =
LTBP3_HUMAN, T;
DR   Q61810, LTBP3_MOUSE, T; Q8K4G1, LTBP4_MOUSE, T; P48740, =
MASP1_HUMAN, T;
DR   P98064, MASP1_MOUSE, T; O00187, MASP2_HUMAN, T; O00339, =
MATN2_HUMAN, T;
DR   O08746, MATN2_MOUSE, T; O95460, MATN4_HUMAN, T; O89029, =
MATN4_MOUSE, T;
DR   P34576, MUA3_CAEEL , T; Q20176, NAS39_CAEEL, T; Q92832, =
NELL1_HUMAN, T;
DR   Q62919, NELL1_RAT  , T; Q99435, NELL2_HUMAN, T; Q61220, =
NELL2_MOUSE, T;
DR   Q62918, NELL2_RAT  , T; Q90827, NEL_CHICK  , T; Q14112, NID2_HUMAN =
, T;
DR   O88322, NID2_MOUSE , T; P14543, NIDO_HUMAN , T; P10493, NIDO_MOUSE =
, T;
DR   P08460, NIDO_RAT   , T; P46530, NOTC1_BRARE, T; P46531, =
NOTC1_HUMAN, T;
DR   Q01705, NOTC1_MOUSE, T; Q07008, NOTC1_RAT  , T; Q04721, =
NOTC2_HUMAN, T;
DR   O35516, NOTC2_MOUSE, T; Q9QW30, NOTC2_RAT  , T; Q9UM47, =
NOTC3_HUMAN, T;
DR   Q61982, NOTC3_MOUSE, T; Q9R172, NOTC3_RAT  , T; Q99466, =
NOTC4_HUMAN, T;
DR   P31695, NOTC4_MOUSE, T; P07207, NOTCH_DROME, T; P21783, =
NOTCH_XENLA, T;
DR   Q28146, NRX1A_BOVIN, T; Q9DDD0, NRX1A_CHICK, T; Q9ULB1, =
NRX1A_HUMAN, T;
DR   Q63372, NRX1A_RAT  , T; Q9Y4C0, NRX3A_HUMAN, T; Q07310, NRX3A_RAT  =
, T;
DR   Q8HYB7, PERT_CANFA , T; P07202, PERT_HUMAN , T; P35419, PERT_MOUSE =
, T;
DR   P14650, PERT_RAT   , T; P13608, PGCA_BOVIN , T; Q28343, PGCA_CANFA =
, T;
DR   P07898, PGCA_CHICK , T; P00745, PROC_BOVIN , T; Q28278, PROC_CANFA =
, T;
DR   P04070, PROC_HUMAN , T; P33587, PROC_MOUSE , T; Q9GLP2, PROC_PIG   =
, T;
DR   Q28661, PROC_RABIT , T; P31394, PROC_RAT   , T; P07224, PROS_BOVIN =
, T;
DR   P07225, PROS_HUMAN , T; Q28520, PROS_MACMU , T; Q08761, PROS_MOUSE =
, T;
DR   P98118, PROS_RABIT , T; P53813, PROS_RAT   , T; P00744, PROZ_BOVIN =
, T;
DR   P22891, PROZ_HUMAN , T; Q9CQW3, PROZ_MOUSE , T; P18168, SERR_DROME =
, T;
DR   O94813, SLIT2_HUMAN, T; P24014, SLIT_DROME , T; Q07929, SP63_STRPU =
, T;
DR   Q26627, SUREJ_STRPU, T; P25723, TLD_DROME  , T; O57460, TLL1_BRARE =
, T;
DR   P06579, TRBM_BOVIN , T; Q5W7P8, TRBM_CANFA , T; P07204, TRBM_HUMAN =
, T;
DR   P15306, TRBM_MOUSE , T; Q71U07, TRBM_SAISC , T; P48733, UROM_BOVIN =
, T;
DR   Q862Z3, UROM_CANFA , T; P07911, UROM_HUMAN , T; Q91X17, UROM_MOUSE =
, T;
DR   P27590, UROM_RAT   , T; P98165, VLDLR_CHICK, T; P98155, =
VLDLR_HUMAN, T;
DR   P98156, VLDLR_MOUSE, T; P35953, VLDLR_RABIT, T; P98166, VLDLR_RAT  =
, T;
DR   P41950, YLK2_CAEEL , T; P98163, YL_DROME   , T;
DR   O15943, CADN_DROME , F; Q13201, MMRN1_HUMAN, F; O75093, =
SLIT1_HUMAN, F;
DR   Q80TR4, SLIT1_MOUSE, F; O88279, SLIT1_RAT  , F; Q9R1B9, =
SLIT2_MOUSE, F;
DR   O75094, SLIT3_HUMAN, F; Q9WVB4, SLIT3_MOUSE, F; O88280, SLIT3_RAT  =
, F;
3D   1APO; 1APQ; 1AUT; 1BF9; 1CCF; 1DAN; 1DVA; 1DX5; 1EDM; 1EMN; 1EMO; =
1F7E;
3D   1F7M; 1FAK; 1FF7; 1FFM; 1GL4; 1HJ7; 1HZ8; 1I0U; 1IXA; 1J9C; 1LMJ; =
1N7D;
3D   1NL8; 1NZI; 1O5D; 1PFX; 1QFK; 1SZB; 1TOZ; 1UZJ; 1UZP; 1UZQ; 1W0Y; =
1WHE;
3D   1WHF; 1XFE; 1XKA; 1XKB;
DO   PDOC00010;
//
  =20

Thanks
Sanjeev

-----Original Message-----
From: Chris Stoeckert [mailto:sto...@pc...]
Sent: Thursday, August 04, 2005 2:56 PM
To: Kumar, Sanjeev (Contr)
Cc: gus...@li...
Subject: Re: [GUSDEV] RE: Gusdev-gusdev digest, Vol 1 #637 - 1 msg


Hi Sanjeev,
I guess the first thing to decide is if this entry represents a =20
sequence, a feature, or an annotation. Do you (or anyone else) have =20
strong opinions on this? Can you send an example entry?
Thanks,
Chris

On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote:

> Hi,
>   Now let us figure out which GUS table to used to store PrositeDB =20
> master data.
>   Can any one help me in that please?
>   Following type of information it contains:
>   ID  Identification (Begins each entry; 1 per entry)
> AC  Accession number (1 per entry)
> DT  Date (1 per entry)
> DE  Short description (1 per entry)
> PA  Pattern (>1 per entry)
> MA  Matrix/profile (>1 per entry)
> RU  Rule (>1 per entry)
> NR  Numerical results (>1 per entry)
> CC  Comments (>=3D1 per entry)
> DR  Cross-references to Swiss-Prot (>1 per entry)
> 3D  Cross-references to PDB (>1 per entry)
> DO  Pointer to the documentation file (1 per entry)
>
> Any help on this will be appreciated.
>
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: gus...@li...
> [mailto:gus...@li...]On Behalf Of
> gus...@li...
> Sent: Tuesday, August 02, 2005 11:09 PM
> To: gus...@li...
> Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg
>
>
> Send Gusdev-gusdev mailing list submissions to
>     gus...@li...
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> or, via email, send a message with subject or body 'help' to
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>
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>
>
> Today's Topics:
>
>    1. RE: Loading Prosite DB (Kumar, Sanjeev (Contr))
>
> --__--__--
>
> Message: 1
> Subject: RE: [GUSDEV] Loading Prosite DB
> Date: Tue, 2 Aug 2005 17:04:05 -0400
> From: "Kumar, Sanjeev \(Contr\)" <San...@ng...>
> To: "Aaron J. Mackey" <am...@pc...>
> Cc: "Jian Lu" <jl...@vb...>,
>     <gus...@li...>
>
> So, The PlugIn which you are writing will not be taking care detail =
=3D
> Prosite data, right?
> If yes then I will write a separate plugin to load detail Prosite =20
> master =3D
> 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 =3D20
> 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
>> =3D20
>> But to load other information for a prosite ID, we need to load =20
>> the =3D20
>> 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=3D99 (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...)
>> =3D96 a filter on top of theBlast package (Altschul, S. F. et al. =20
>> 1997) =3D
>>
> .
>
>>
>>   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
>>
>> =3DD8     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
>>
>>
>>
>>
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>>
>
> --
> 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
>
>
>
>
>
> --__--__--
>
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