kfetchdata

 

Function

Fetch an entry in a defined format and style

Description

kfetchdata fetches an entry in a defined format and style using dbfetch service. dbfetch allows you to retrieve entryies from various up-to-date biological databases using entry identifires or accession numbers.

kfetchdata utilizes fetchdata method included dbfetch SOAP service provided
EBI (European Bioinformatics Institute). Original web-service is located at the following URL:

http://www.ebi.ac.uk/cgi-bin/dbfetch

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kfetchdata is thus an interface of "runFetchData" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kfetchdata

% kfetchdata
Fetch an entry in a defined format and style
dbName:ID: UniProtKB:WAP_RAT
Output file [outfile.kfetchdata]: 
Jobid: kbws_12654644
***


ID   WAP_RAT                 Reviewed;         137 AA.
AC   P01174;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1989, sequence version 2.
DT   24-NOV-2009, entry version 79.
DE   RecName: Full=Whey acidic protein;
DE   AltName: Full=Whey phosphoprotein;
DE   AltName: Full=WAP;
DE   Flags: Precursor;
GN   Name=Wap;
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi;
OC   Muroidea; Muridae; Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=85062841;
 PubMed=6095207; DOI=10.1093/nar/12.22.8685;
RA   Campbell S.M., Rosen J.M., Hennighausen L.G., Strech-Jurk U.,
RA   Sippel A.E.;
RT   "Comparison of the whey acidic protein genes of the rat and mouse.";
RL   Nucleic Acids Res. 12:8685-8697(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   MEDLINE=82274212;
 PubMed=6896749; DOI=10.1093/nar/10.12.3733;
RA   Hennighausen L.G., Sippel A.E.;
RT   "Comparative sequence analysis of the mRNAs coding for mouse and rat
RT   whey protein.";
RL   Nucleic Acids Res. 10:3733-3744(1982).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 20-41, AND DISULFIDE
RP   BONDS.
RX   MEDLINE=82275050;
 PubMed=6955785; DOI=10.1073/pnas.79.13.3987;
RA   Dandekar A.M., Robinson E.A., Appella E., Qasba P.K.;
RT   "Complete sequence analysis of cDNA clones encoding rat whey
RT   phosphoprotein: homology to a protease inhibitor.";
RL   Proc. Natl. Acad. Sci. U.S.A. 79:3987-3991(1982).
CC   -!- FUNCTION: Could be a protease inhibitor.
CC   -!- SUBCELLULAR LOCATION: Secreted.
CC   -!- TISSUE SPECIFICITY: Milk-specific; major protein component of milk
CC       whey.
CC   -!- PTM: Contains 8 disulfide bonds.
CC   -!- SIMILARITY: Contains 2 WAP domains.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; X01153; CAA25600.2
; -; Genomic_DNA.
DR   EMBL; X01154; CAA25600.2
; JOINED; Genomic_DNA.
DR   EMBL; X01155; CAA25600.2
; JOINED; Genomic_DNA.
DR   EMBL; X01156; CAA25600.2
; JOINED; Genomic_DNA.
DR   EMBL; J00801; AAA42346.1
; -; mRNA.
DR   IPI; IPI00210939; -.
DR   PIR; A93920; WYRT.
DR   RefSeq; NP_446203.1; -.
DR   UniGene; Rn.9978; -.
DR   STRING; P01174; -.
DR   Ensembl; ENSRNOT00000010744
; ENSRNOP00000010744; ENSRNOG00000008097; Rattus norvegicus.
DR   GeneID; 114596; -.
DR   KEGG; rno:114596; -.
DR   UCSC; NM_053751; rat.
DR   CTD; 114596; -.
DR   RGD; 621851; Wap.
DR   HOVERGEN; P01174; -.
DR   NextBio; 618763; -.
DR   ArrayExpress; P01174; -.
DR   Genevestigator; P01174;
 -.
DR   GermOnline; ENSRNOG00000008097;
 Rattus norvegicus.
DR   GO; GO:0005576; C:extracellular region; IEA:UniPro
tKB-SubCell.
DR   GO; GO:0030414; F:peptidase inhibitor activity; NA
S:RGD.
DR   InterPro; IPR015874; 4-disulph
ide_core.
DR   InterPro; IPR008197; Whey_acid
ic_protein_4-diS_core.
DR   Gene3D; G3DSA:4.10.75.10; Whey_acidic_protein_4-diS_core; 1
.
DR   Pfam; PF00095; WAP; 2.
DR   PRINTS; PR00003; 4DISULPHCORE.
DR   SMART; SM00217; WAP; 1.
DR   PROSITE; PS51390; WAP; 2.
PE   1: Evidence at protein level;
KW   Direct protein sequencing; Disulfide bond; Milk protein;
KW   Protease inhibitor; Repeat; Secreted; <
A HREF=http://www.expasy.org/cgi-bin/get-entries?KW=Signal>Signal.
FT   SIGNAL        1     19
FT   CHAIN        20    137       Wh
ey acidic protein.
FT                                /FTId=PRO_0000041353.
FT   DOMAIN       27     73       WA
P 1.
FT   DOMAIN       76    127       WA
P 2.
FT   DISULFID     34     61       Pr
obable.
FT   DISULFID     45     65       Pr
obable.
FT   DISULFID     48     60       Pr
obable.
FT   DISULFID     54     69       Pr
obable.
FT   DISULFID     83    115       Pr
obable.
FT   DISULFID     96    119       P
robable.
FT   DISULFID    102    114       P
robable.
FT   DISULFID    108    123       P
robable.
FT   CONFLICT      4      4       S
 -> F (in Ref. 3; AAA42347).
FT   CONFLICT     35     35       S
 -> P (in Ref. 2 and 3).
FT   CONFLICT     39     39       F
 -> S (in Ref. 2 and 3).
FT   CONFLICT     47     47       N
 -> K (in Ref. 2; AAA42346).
FT   CONFLICT     68     68       S
 -> P (in Ref. 2 and 3).
FT   CONFLICT     99     99       D
 -> G (in Ref. 2; AAA42346).
FT   CONFLICT    116    116       K
 -> N (in Ref. 2 and 3).
FT   CONFLICT    127    127       E
 -> K (in Ref. 2).
FT   CONFLICT    129    129       K
 -> D (in Ref. 2).
FT   CONFLICT    129    129       K
 -> E (in Ref. 3; AAA42347).
FT   CONFLICT    134    134       I
 -> V (in Ref. 3; AAA42347).
SQ   SEQUENCE   137 AA;  14827 MW;  1C2E8ADA9FD97949 CRC64;
     MRCSISLVLG LLALEVALAR NLQEHVFNSV QSMCSDDSFS EDTECINCQT NEECAQNDMC
     CPSSCGRSCK TPVNIEVQKA GRCPWNPIQM IAAGPCPKDN PCSIDSDCSG TMKCCKNGCI
     MSCMDPEPKS PTVISFQ
//




Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-id]
(Parameter 1)
string dbName:ID Any string 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kfetchdata
Additional (Optional) qualifiers
-format string output format Any string default
-style string output data style Any string default
Advanced (Unprompted) qualifiers
(none)

Input file format

kfetchdata can use any genome sequence data that seqret can read.

Output file format

The output of kfetchdata is strings containing the entry. Generally this will contain only one item which contains the whole entry.

Data files

None.

Notes

None.

References


   Labarga, A., et al.,(2007) Web Services at the European Bioinformatics
      Institute, Nucleic Acids Research, 35, W6-W11.


Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments