1. Swiss-Prot Database --- Xie, H
Hongbo Xie
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H

2. Swiss-Prot Database --- Xie, H
Presentation Outline
Background Introduction
Swiss-Prot database Features
Building local Swiss-Prot database
Experiments and Results
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H

3. Swiss-Prot Database --- Xie, H
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H

4. An Example of protein data
Sequence information
Structure information
Function information
Gene information
Name in order to search
Link to other database
Paper reference
Others.
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Swiss-Prot Database --- Xie, H

5. Swiss-Prot Database --- Xie, H
Metadata
ID 11SB_CUCMA STANDARD; PRT; AA.
AC P13744;
DT 01-JAN-1990 (REL. 13, CREATED)
DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)
DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)
DE 11S GLOBULIN BETA SUBUNIT PRECURSOR.
OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).
OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;
OC VIOLALES; CUCURBITACEAE.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;
RX MEDLINE;
RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;
RL EUR. J. BIOCHEM. 172: (1988).
RN [2]
RP SEQUENCE OF AND
RA OHMIYA M., HARA I., MASTUBARA H.;
RL PLANT CELL PHYSIOL. 21: (1980).
CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.
CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND A
CC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY A
CC DISULFIDE BOND.
CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).
DR EMBL; M36407; G167492; -.
DR PIR; S00366; FWPU1B.
DR PROSITE; PS00305; 11S_SEED_STORAGE; 1.
KW SEED STORAGE PROTEIN; SIGNAL.
FT SIGNAL
FT CHAIN S GLOBULIN BETA SUBUNIT.
FT CHAIN GAMMA CHAIN (ACIDIC).
FT CHAIN DELTA CHAIN (BASIC).
FT MOD_RES PYRROLIDONE CARBOXYLIC ACID.
FT DISULFID INTERCHAIN (GAMMA-DELTA) (POTENTIAL).
FT CONFLICT S -> E (IN REF. 2).
FT CONFLICT E -> S (IN REF. 2).
SQ SEQUENCE AA; MW; D515DD6E CRC32;
MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR
RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA
EAFQIDGGLV RKLKGEDDER DRIVQVDEDF EVLLPEKDEE ERSRGRYIES ESESENGLEE
TICTLRLKQN IGRSVRADVF NPRGGRISTA NYHTLPILRQ VRLSAERGVL YSNAMVAPHY
TVNSHSVMYA TRGNARVQVV DNFGQSVFDG EVREGQVLMI PQNFVVIKRA SDRGFEWIAF
KTNDNAITNL LAGRVSQMRM LPLGVLSNMY RISREEAQRL KYGQQEMRVL SPGRSQGRRE //
Swissprot -- a curetted database
(1 of ~100,000 entries)
...
OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).
OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;
OC VIOLALES; CUCURBITACEAE.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;
RX MEDLINE;
RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;
RL EUR. J. BIOCHEM. 172: (1988).
DT 01-JAN-1990 (REL. 13, CREATED)
DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)
DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)
Recordof history
Sequence Data
MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR
RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA
IPGCAETYQT DLRRSQSAGS AFKDQHQKIR PFREGDLLVV PAGVSHWMYN RGQSDLVLIV
FADTRNVANQ IDPYLRKFYL AGRPEQVERG VEEWERSSRK GSSGEKSGNI FSGFADEFLE
...
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Swiss-Prot Database --- Xie, H

6. Swiss-Prot Database --- Xie, H
SwissProt web search
ID,AC,etc
143B_HUMAN
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Swiss-Prot Database --- Xie, H

7. Web search can not do everything, we definitely
Find the single entry. But how about I try to find all proteins with same ProtoMap Index
Web search can not do everything, we definitely
Need some improvement.
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H

8. Swiss-Prot Database --- Xie, H
Our Research
Goal: Study the whole SwissProt database in order to find out the relationship between the protein sequence, protein structure and function.
Tool: MATLAB
Methodology : Building Localized Swiss-Prot database in MS SQL Server to accelerate the research
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H

9. Connection between Matlab and Database
Data could be moved between Matlab and Database
Import
Matlab
Database
Export
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Swiss-Prot Database --- Xie, H

10. Local SwissProt Database Schema
KW table
ProtoMap Table ID KW ID
ProtM_ID
DR table
Protein Table
Prediction Table ID DR ID NO ID C
Pfam Table
SEQ V S
LENGTH ID
Pfam_ID
VL2
VL3
VL4
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Swiss-Prot Database --- Xie, H

11. Search within our database
Back to the old question, instead of questions like single query, we can try some queries for a summary report. Q:
“List the proteins’ IDs with the ProtoMap family index = ‘840’ “
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Swiss-Prot Database --- Xie, H

12. Type “querybuilder” in command window
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Swiss-Prot Database --- Xie, H

13. select distinct id from protomap where protfam=‘840’
Select variable name we try to collect
Select certain table name
Select DB name
select distinct id from protomap where protfam=‘840’
Matlab varible hold the result
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Swiss-Prot Database --- Xie, H

14. Swiss-Prot Database --- Xie, H
Result
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Swiss-Prot Database --- Xie, H

15. Swiss-Prot Database --- Xie, H
Feedback/Questions ?
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Swiss-Prot Database --- Xie, H

16. Swiss-Prot Database --- Xie, H
THANK YOU !
9/22/2018 4:59:40 PM
Swiss-Prot Database --- Xie, H