[BioRuby] Parsing a file in Swissprot format

n at bioruby.org n at bioruby.org
Fri Dec 2 22:41:04 EST 2005


Hi Uarban,


Your input file is a entry (SM0000001) in S/MARt DB.

* S/MARt DB
  http://smartdb.bioinf.med.uni-goettingen.de/SMARtDB/browse/index.html

* SM0000001
  http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?SM0000001


> 
> Here's my input file:
> 
> AC   SM0000001
> XX   
> DT   1.1.1999 00:00:00 (created); ili
> DT   8.12.2004 12:49:00 (updated); ili2
> XX   
> NA   MOUSE$kappa-MAR
> XX   
> OS   mouse, Mus spec.
> OC   eukaryota; animalia; metazoa; chordata; vertebrata;
> OC   tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae;
> OC   murinae
> XX   
> HO   human, rabbit [2]
> XX   
> SZ   371 bp
> XX   
> DE   G000538; immunoglobulin kappa light chain
> DP   Direction: 3'; Pos 1: ATG
> DN   Internal: y; 
> DC   between joining and constant regions [1]; ~200 bp
> DC   upstream of the kappa enhancer [1]
> XX   
> SQ   AAGCTTAATGTATATAATCTTTTAGAGGTAAAATCTACAGCCAGCAAAAGTCATGGTAAA
> SQ   TATTCTTTGACTGAACTCTCACTAAACTCCTCTAAATTATATGTCATATTAACTGGTTAA
> SQ   ATTAATATAAATTTGTGACATGACCTTAACTGGTTAGGTAGGATATTTTTCTTCATGCAA
> SQ   AAATATGACTAATAATAATTTAGCACAAAAATATTTCCCAATACTTTAATTCTGTGATAG
> SQ   AAAAATGTTTAACTCAGCTACTATAATCCCATAATTTTGAAAACTATTTATTAGCTTTTG
> SQ   TGTTTGACCCTTCCCTAGCCAAAGGCAACTATTTAAGGACCCTTTAAAACTCTTGAAACT
> SQ   ACTTTAGAGTC
> SC   [7]
> XX   
> FT   2 - 11: cleavage by topoisomerase II [3]
> FT   2 - 15: deleted in plasmacytoma PC 7183 [3]
> FT   5 - 14: cleavage by topoisomerase II [3]
> FT   5 - 14: 5'-recombination junction [3]
> FT   8 - 17: cleavage by topoisomerase II [3]
> FT   10 - 19: cleavage by topoisomerase II [3]
> FT   32 - 41: cleavage by topoisomerase II [3]
> FT   53 - 62: cleavage by Drosophila topoisomerase II only
> FT   [3]
> FT   68 - 77: cleavage by topoisomerase II [3]
> FT   69 - 78: cleavage by topoisomerase II [3]
> FT   73 - 82: cleavage by topoisomerase II [3]
> FT   98 - 107: cleavage by Drosophila topoisomerase II only
> FT   [3]
> FT   147 - 156: cleavage by topoisomerase II [3]
> FT   163 - 284: confers MAR-like features upon any DNA when
> FT   contiguously reiterated in the same molecule
> FT   [7]
> FT   164 - 170: similar motif found in human PARP MAR
> FT   SM0000116 [8]
> FT   182 - 191: cleavage by topoisomerase II [3]
> FT   189 - 198: cleavage by topoisomerase II [3]
> FT   219 - 228: cleavage by topoisomerase II [3]
> FT   242 - 251: cleavage by topoisomerase II [3]
> FT   248 - 257: cleavage by topoisomerase II [3]
> FT   253 - 253: G in [3]
> FT   256 - 265: cleavage by topoisomerase II [3]
> XX   
> SF   topoisomerase II sites [1]; AT-rich sites [1];
> SF   contains a breakpoint for chromosomal translocation [3];
> SF   several short stretches of homopolymeric adenine or
> SF   thymine [7]
> XX   
> BP   75% [J. Bode, direct submission]; 20% [7]
> TP   constitutive [1]
> XX   
> FF   prototype of a S/MAR; contributes to maximal expression of
> FF   the kappa gene [2]; contributes to hypermutation [9];
> FF   contributes to kappa expression as shown by flow cytometic
> FF   assay, but has little effect on accumulation of the
> FF   respective mRNA [9]
> XX   
> CP   liver, kidney, spleen, thymus, MPC-11, P-815, L-cell [1]
> XX   
> EV   in vitro selection of S/MAR 
> EC   [J. Bode, direct submission]
> XX   
> BF   SB000002; lamin A [6]
> MM   nitrocellulose filter binding; 
> SO   rl; rat
> QA   6
> BF   SB000003; lamin B1 [6]
> MM   nitrocellulose filter binding; 
> SO   rl; rat
> QA   6
> BF   SB000004; lamin C [6]
> MM   nitrocellulose filter binding; 
> SO   rl; rat
> QA   6
> BF   SB000018; SP120 [4]
> MM   nitrocellulose filter binding; 
> SO   brain; rat
> QA   6
> BF   SB000018; SP120 [4]
> MM   southwestern blotting; 
> SO   brain; rat
> QA   6
> BF   SB000022; topoisomerase II [3]
> MM   gel retardation; 
> SO   Drosophila; Drosophila melanogaster
> QA   6
> BF   SB000022; topoisomerase II [3]
> MM   topoisomerase II cleavage assay; 
> SO   Drosophila; Drosophila melanogaster
> QA   6
> BF   SB000043; topoisomerase II [3]
> MM   topoisomerase II cleavage assay; 
> SO   calf; calf
> QA   6
> BF   SB000045; SMI1 [5]
> MM   functional analysis; 
> PR   254 bp fragment
> SO   yeast, extract; baker's yeast, Saccharomyces cerevisiae
> QA   6
> BF   SB000052; topoisomerase II [3]
> MM   topoisomerase II cleavage assay; 
> SO   mouse; mouse
> QA   6
> BF   SB000053; topoisomerase II [3]
> MM   nitrocellulose filter binding; 
> SO   HeLa; human
> QA   6
> BF   SB000067; SMAR1 [10]
> MM   gel shift competition; 
> SO   rec(mouse-E.coli); mouse
> QA   6
> BF   SB000077; SAF-A [12]
> MM   supershift (antibody binding); 
> SO   liver; mouse
> QA   6
> BF   SB000077; SAF-A [12]
> MM   southwestern blotting; 
> SO   liver; mouse
> QA   6
> XX   
> RN   [1]
> RX   MEDLINE; 86106203 PubMed; 3002631
> RA   Cockerill, P. N., Garrard, W. T.
> RT   Chromosomal loop anchorage of the kappa immunoglobin gene
> RT   occurs next to the enhancer in a region containing
> RT   topoisomerase II sites
> RL   Cell 44:273-282 (1986)
> RN   [2]
> RX   MEDLINE; 90078219 PubMed; 2512290
> RA   Blasquez, V. C., Xu, M., Moses, S. C., Garrard, W. T.
> RT   Immunoglobulin kappa gene expression after stable
> RT   integration. I. Role of the intronic MAR and enhancer in
> RT   plasmacytoma cells
> RL   J. Biol. Chem. 264:21183-21189 (1989)
> RN   [3]
> RX   MEDLINE; 89315824 PubMed; 2546156
> RA   Sperry, A. O., Blasquez, V. C., Garrard, W. T.
> RT   Dysfunction of chromosomal llop attachment sites:
> RT   Illegitimate recombination linked to matrix association
> RT   regions and topoisomerase II
> RL   Proc. Natl. Acad. Sci. USA 86:5497-5501 (1989)
> RN   [4]
> RX   MEDLINE; 93286136 PubMed; 8509422
> RA   Tsutsui, K., Tsutsui, K., Okada, S., Watarai, S., Seki, S.,
> RA   Yasuda, T., Shohmori, T.
> RT   Identification and characterization of a nuclear scaffold
> RT   protein that binds the matrix attachment region DNA
> RL   J. Biol. Chem. 268:12886-12894 (1993)
> RN   [5]
> RX   MEDLINE; 93296190 PubMed; 8516310
> RA   Fishel, B. R., Sperry, A. O., Garrard, W. T.
> RT   Yeast calmodulin and a conserved nuclear protein
> RT   participate in the in vivo binding of a matrix associated
> RT   region
> RL   Proc. Natl. Acad. Sci. USA 90:5623-5627 (1993)
> RN   [6]
> RX   MEDLINE; 94344140 PubMed; 8065361
> RA   Luderus, M. E. E., den Blaauwen, J. L., de Smit, O. J. B.,
> RA   Compton, D. A., van Driel, R.
> RT   Binding of matrix attachment regions to lamin polymers
> RT   involves single-stranded regions and the minor groove
> RL   Mol. Cell. Biol. 14:6297-6305 (1994)
> RN   [7]
> RX   MEDLINE; 96222527 PubMed; 8670229
> RA   Okada, S., Tsutsui, K., Tsutsui, K., Seki, S., Shohmori, T.
> RT   Subdomain structure of the matrix attachment region located
> RT   within the mouse immunoglobulin kappa gene intron
> RL   Biochem. Biophys. Res. Commun. 222:472-477 (1996)
> RN   [8]
> RA   Boulikas, T., Kong, C. F., Brooks, D., Hsie, L.
> RT   The 3' untranslated region of the human
> RT   poly(ADP-ribose)polymerase gene is a nuclear matrix
> RT   anchoring site
> RL   Int. J. Oncol. 9:1287-1294 (1996)
> RN   [9]
> RX   MEDLINE; 97377037 PubMed; 9233808
> RA   Goyenechea, B., Klix, N., Williams, G. T., Riddell, A.,
> RA   Neuberger, M. S., Milstein, C.
> RT   Cells strongly expressing Ig kappa transgenes show clonal
> RT   recruitment of hypermutation: a role for both MAR and the
> RT   enhancers
> RL   EMBO J. 16:3987-3994 (1997)
> RN   [10]
> RX   MEDLINE; 20408892 PubMed; 10950932
> RA   Chattopadhyay, S., Kaul, R., Charest, A., Housman, D.,
> RA   Chen, J.
> RT   SMAR1, a novel, alternatively spliced gene product, binds
> RT   the scaffold/matrix-associated region at the T cell
> RT   receptor beta locus
> RL   Genomics 68:93-96 (2000)
> RN   [11]
> RX   MEDLINE; 20496822 PubMed; 11041885
> RA   Morisawa, G., Han-yama, A., Moda, I., Tamai, A., Iwabuchi,
> RA   M., Meshi, T.
> RT   AHM1, a novel type of nuclear matrix-localized, MAR binding
> RT   protein with a single AT hook and a J
> RT   domain-homologous region
> RL   Plant Cell 12:1903-1916 (2000)
> RN   [12]
> RX   MEDLINE; 21456956 PubMed; 11573239
> RA   Lobov, I. B., Tsutsui, K., Mitchell, A. R., Podgornaya, O.
> RA   I.
> RT   Specificity of SAF-A and lamin B binding in vitro
> RT   correlates with the satellite DNA bending state
> RL   J. Cell. Biochem. 83:218-229 (2001)
> //


Best,
Mitsuteru
-
<n at bioruby.org>


Mitsuteru Nakao                            <nakao-mitsuteru at aist.go.jp>
                                         <http://seq.cbrc.jp/%7Enakao/>
Sequence Analysis Team                             <http://seq.cbrc.jp>
Compuational Biology Research Center (CBRC)        <http://www.cbrc.jp>
National Institute of Advanced Industrial Science and Technology (AIST)


BioRuby Project <http://bioruby.org>
b-Src <http://b-Src.cbrc.jp/markup>


More information about the BioRuby mailing list