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Deprecating Bio.InterPro since it doesn't work with the current EBI I…

…nterPro website and uses the deprecate sgmllib module
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commit 9971d2ca170ab7ba2d084b1d65d31c143c7df1b4 1 parent dcb66ed
@peterjc peterjc authored
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7 Bio/InterPro/__init__.py
@@ -18,6 +18,11 @@
"""
+import warnings
+warnings.warn("Bio.InterPro is deprecated, and will be removed in a future "
+ "release of Biopython. Please get in contact via the mailing "
+ "lists if this is a problem for you.", DeprecationWarning)
+
from Bio import File
import sgmllib
from Bio.SeqFeature import Reference
@@ -257,7 +262,7 @@ def get_interpro_entry( id ):
if __name__ == '__main__':
import Bio.File
- handle = open('IPR001064.htm')
+ handle = get_interpro_entry('IPR001064')
undo_handle = Bio.File.UndoHandle( handle )
interpro_parser = InterProParser()
record = interpro_parser.parse( handle )
View
5 DEPRECATED
@@ -16,6 +16,11 @@ support for Python 2.4. This can be delayed given feedback from our users
(e.g. if this proves to be a problem in combination with other libraries).
An explicit warning was added to setup.py for Biopython 1.55.
+Bio.InterPro
+============
+This module was a parser for the EBI InterPro webpages, but no longer works
+with their current website. Deprecated in Release 1.55.
+
Bio.GenBank.LocationParser
==========================
This module used to be used for parsing GenBank and EMBL feature locations.
View
104 Tests/InterPro/IPR001064.htm
@@ -1,104 +0,0 @@
-<!doctype html public "-//W3C//DTD HTML 4.0//EN">
-<html><head>
-<link rel="stylesheet" href="ipa_styles.css" type="text/css">
-<title>InterPro Entry IPR001064</title></head>
-<body bgcolor=white>
-<a border=0 href="index.html">
-<img border=0 src="images/interpro_logo.jpeg"></a>
-<table width=600 class=frame border=0><tr><td><table border=0 width=100% cellspacing=1 cellpadding=3><tr><td class=tag>InterPro Entry IPR001064</td></tr></table></td></tr></table>
-<h2 class=name>Crystallin</h2>
-<table class=frame border=0 width="100%"><tr><td>
-<table border=0 cellspacing=1 cellpadding=3 width=100%>
-<tr>
-<td class=tag valign=top width=110>Database</td>
-<td class=inf valign=top width=1200>InterPro</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Accession</td>
-<td class=inf valign=top width=1200>IPR001064; Crystallin (matches 132 proteins)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Name</td>
-<td class=inf valign=top width=1200>Crystallin</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Type</td>
-<td class=inf valign=top width=1200><A href="#" onClick='w=window.open("IHelpServlet?help=Domain", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Domain
-<img src="gifs/help.gif" width=19 height=19 border=0 alt=""></a></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Dates</td>
-<td class=inf valign=top width=1200>08-OCT-1999 (created)<BR>05-DEC-2000 (last modified)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Signatures</td>
-<td class=inf valign=top width=1200>
-<a href="http://www.expasy.ch/cgi-bin/nicesite.pl?PS00225">PS00225</a>; CRYSTALLIN_BETAGAMMA
- (1586 proteins)<br><a href="http://methionine.sbc.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=PR01367">PR01367</a>; BGCRYSTALLIN
- (102 proteins)<br><a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00030">PF00030</a>; crystall
- (113 proteins)<br><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=XTALbg&BLAST=DUMMY">SM00247</a>; XTALbg
- (129 proteins)<br></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=abstract", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Abstract
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>Crystallins are the dominant structural components of the eye lens. Among the
-different type of crystallins, the beta and gamma crystallins form a family of
-related proteins [1, 2]. Structurally, beta and gamma crystallins
-are composed of two similar domains which, in turn, are each composed of two similar
-motifs with the two domains connected by a short connecting peptide. Each motif,
-which is about forty amino acid residues long, is folded in a distinctive
-'Greek key' pattern.</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Examples</td>
-<td class=inf valign=top width=1200><ul>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P02966]">P02966</a> DESS_MYXXA: A calcium-binding protein from the sporulating bacterium Myxococcus xanthusa forms a major part of the spore coat</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P46058]">P46058</a> EDSP_CYNPY</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P09353]">P09353</a> SR3A_PHYPO: Spherulin 3a from the slime mold Physarum polycephalum. Spherulin 3a is a development specific protein synthesized in response to various kinds of stress leading to encystment and dormancy. The sequence of Spherulin 3a consists of two 'Greek key' motifs [3]</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P06504]">P06504</a> CRBS_BOVIN</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:Q91314]">Q91314</a> CB12_RANCA</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P07317]">P07317</a> CRBA_RANTE</li>
-<br><a href="ISpy?ac=P02966,P46058,P09353,P06504,Q91314,P07317">View examples</a>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>References</td>
-<td class=inf valign=top width=1200><ol>
-<li value=1><a name=PUB00000056>
-Wistow G.J., Piatigorsky J.<br>
-<i>Lens crystallins: the evolution and expression of proteins for a highly specialized tissue.</i><br>
-Annu. Rev. Biochem. 57: 479-504(1988).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=89024580&form=6&db=m&Dopt=b">[MEDLINE:89024580]</a>
-[PUB00000056]
-
-<li value=2><a name=PUB00004933>
-Lubsen N.H., Aarts H.J.M., Schoenmakers J.G.G.<br>
-<i>The evolution of lenticular proteins: the beta- and gamma-crystallin super gene family.</i><br>
-Prog. Biophys. Mol. Biol. 51: 47-76(1988).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=89113769&form=6&db=m&Dopt=b">[MEDLINE:89113769]</a>
-[PUB00004933]
-
-<li value=3><a name=PUB00003409>
-Wistow G.<br>
-<i>Evolution of a protein superfamily: relationships between vertebrate lens crystallins and microorganism dormancy proteins.</i><br>
-J. Mol. Evol. 30: 140-145(1990).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=90189184&form=6&db=m&Dopt=b">[MEDLINE:90189184]</a>
-[PUB00003409]
-</ol></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Database links</td><td class=inf valign=top width=1200>
-PROSITE doc; <a href="http://www.expasy.ch/cgi-bin/nicedoc.pl?PDOC00197">PDOC00197</a><br>
-Blocks; <a href="http://blocks.fhcrc.org/blocks-bin/getblock.sh?IPB001064">IPB001064</a><br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=matches", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Matches
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><a href="ISpy?ipr=IPR001064&display=n">Table</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001064&display=n&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001064">Graphical</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001064&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="http://www.ebi.ac.uk/~flo/cgi-bin/InterPro_GUI/script/ReqInterPro.pl?list_ipr_ac=IPR001064">Condensed graphical view</a></td></tr>
-
-</table></td></tr></table>
View
93 Tests/InterPro/IPR001171.htm
@@ -1,93 +0,0 @@
-<!doctype html public "-//W3C//DTD HTML 4.0//EN">
-<html><head>
-<link rel="stylesheet" href="ipa_styles.css" type="text/css">
-<title>InterPro Entry IPR001171</title></head>
-<body bgcolor=white>
-<a border=0 href="index.html">
-<img border=0 src="images/interpro_logo.jpeg"></a>
-<table width=600 class=frame border=0><tr><td><table border=0 width=100% cellspacing=1 cellpadding=3><tr><td class=tag>InterPro Entry IPR001171</td></tr></table></td></tr></table>
-<h2 class=name>Ergosterol biosynthesis ERG4/ERG24 enzymes</h2>
-<table class=frame border=0 width="100%"><tr><td>
-<table border=0 cellspacing=1 cellpadding=3 width=100%>
-<tr>
-<td class=tag valign=top width=110>Database</td>
-<td class=inf valign=top width=1200>InterPro</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Accession</td>
-<td class=inf valign=top width=1200>IPR001171; ERG4_ERG24 (matches 29 proteins)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Name</td>
-<td class=inf valign=top width=1200>Ergosterol biosynthesis ERG4/ERG24 enzymes</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Type</td>
-<td class=inf valign=top width=1200><A href="#" onClick='w=window.open("IHelpServlet?help=Family", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Family
-<img src="gifs/help.gif" width=19 height=19 border=0 alt=""></a></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Dates</td>
-<td class=inf valign=top width=1200>08-OCT-1999 (created)<BR>14-NOV-2000 (last modified)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Signatures</td>
-<td class=inf valign=top width=1200>
-<a href="http://www.expasy.ch/cgi-bin/nicesite.pl?PS01017">PS01017</a>; ERG4_ERG24_1
- (16 proteins)<br><a href="http://www.expasy.ch/cgi-bin/nicesite.pl?PS01018">PS01018</a>; ERG4_ERG24_2
- (13 proteins)<br><a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF01222">PF01222</a>; ERG4_ERG24
- (29 proteins)<br></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=cellularcomponent", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Component
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>membrane (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0016020">GO:0016020</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=abstract", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Abstract
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>The two <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=4751>fungal</a> enzymes, C-14 sterol reductase (gene ERG24 in <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=4892>budding yeast</a> and erg3 in
-<a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=5141>Neurospora Crassa</a>) and C-24(28) sterol reductase (gene ERG4 in <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=4892>budding yeast</a> and sts1
-in <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=4896>fission yeast</a>), are involved in ergosterol biosynthesis. They act by reducing
-double bonds in precursors of ergosterol [1].
-These proteins are highly hydrophobic and seem to contain seven or eight transmembrane
-regions. <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=9031>Chicken</a> lamin B receptor that is thought to anchor the lamina to the inner
-nuclear membrane belongs to this family.</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Examples</td>
-<td class=inf valign=top width=1200><ul>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P38670]">P38670</a> ER24_NEUCR</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P23913]">P23913</a> LBR_CHICK</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P36209]">P36209</a> STS1_SCHPO</li>
-<br><a href="ISpy?ac=P38670,P23913,P36209">View examples</a>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>References</td>
-<td class=inf valign=top width=1200><ol>
-<li value=1><a name=PUB00001844>
-Lai M.H., Bard M., Pierson C.A., Alexander J.F., Goebl M., Carter G.T., Kirsch D.R.<br>
-<i>The identification of a gene family in the Saccharomyces cerevisiae ergosterol biosynthesis pathway.</i><br>
-Gene 140: 41-49(1994).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=94171077&form=6&db=m&Dopt=b">[MEDLINE:94171077]</a>
-[PUB00001844]
-</ol></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Database links</td><td class=inf valign=top width=1200>
-PROSITE doc; <a href="http://www.expasy.ch/cgi-bin/nicedoc.pl?PDOC00780">PDOC00780</a><br>
-Blocks; <a href="http://blocks.fhcrc.org/blocks-bin/getblock.sh?IPB001171">IPB001171</a><br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=matches", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Matches
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><a href="ISpy?ipr=IPR001171&display=n">Table</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001171&display=n&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001171">Graphical</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001171&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="http://www.ebi.ac.uk/~flo/cgi-bin/InterPro_GUI/script/ReqInterPro.pl?list_ipr_ac=IPR001171">Condensed graphical view</a></td></tr>
-
-</table></td></tr></table>
View
112 Tests/InterPro/IPR001391.htm
@@ -1,112 +0,0 @@
-<!doctype html public "-//W3C//DTD HTML 4.0//EN">
-<html><head>
-<link rel="stylesheet" href="ipa_styles.css" type="text/css">
-<title>InterPro Entry IPR001391</title></head>
-<body bgcolor=white>
-<a border=0 href="index.html">
-<img border=0 src="images/interpro_logo.jpeg"></a>
-<table width=600 class=frame border=0><tr><td><table border=0 width=100% cellspacing=1 cellpadding=3><tr><td class=tag>InterPro Entry IPR001391</td></tr></table></td></tr></table>
-<h2 class=name>Lateral eye opsin</h2>
-<table class=frame border=0 width="100%"><tr><td>
-<table border=0 cellspacing=1 cellpadding=3 width=100%>
-<tr>
-<td class=tag valign=top width=110>Database</td>
-<td class=inf valign=top width=1200>InterPro</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Accession</td>
-<td class=inf valign=top width=1200>IPR001391; Opsin_lateye (matches 23 proteins)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Name</td>
-<td class=inf valign=top width=1200>Lateral eye opsin</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Type</td>
-<td class=inf valign=top width=1200><A href="#" onClick='w=window.open("IHelpServlet?help=Family", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Family
-<img src="gifs/help.gif" width=19 height=19 border=0 alt=""></a></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Dates</td>
-<td class=inf valign=top width=1200>08-OCT-1999 (created)<BR>27-NOV-2000 (last modified)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Signatures</td>
-<td class=inf valign=top width=1200>
-<a href="http://methionine.sbc.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=PR00578">PR00578</a>; OPSINLTRLEYE
- (23 proteins)<br></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=parent", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Parent
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a><br><a href="ITreeDisplay?ipr=IPR001391">[tree]</a></td><td class=inf valign=top width=1200>
-<a href="/interpro/IEntry?ac=IPR001760">IPR001760</a>; Opsin (358 proteins)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=biologicalprocess", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Process
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>phototransduction (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0007602">GO:0007602</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=molecularfunction", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Function
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>G-protein coupled receptor (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0004930">GO:0004930</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=cellularcomponent", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Component
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>membrane (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0016020">GO:0016020</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=abstract", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Abstract
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><p>Opsins are the photoreceptors of <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=33208>animal</a> retinas [1]: <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=7742>vertebrate</a> rhodopsin
-is found in rod cells and mediates scotopic vision; red, green and blue
-opsins are found in cone cells and mediate photopic vision. The opsins from
-the lateral eyes and median ocelli of the horseshoe crab, <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=6850>Limulus polyphemus</a>,
-are likely to be the visible-wavelength rhodopsins in this animal [2]. In
-the lateral eye, expression of the opsin gene is restricted to the photoreceptor cells of the ommatidia [2]. <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=6849>Limulus</a> opsins, and closely-related
-<a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=6724>crayfish</a>, mantid and <a href=http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?lvl=0&id=7460>honeybee</a> rhodopsins, are most similar to the opsin
-from the R1-6 photoreceptors of flies.</p></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Examples</td>
-<td class=inf valign=top width=1200><ul>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:Q94741]">Q94741</a> OPS1_SCHGR</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P35360]">P35360</a> OPS1_LIMPO</li>
-<br><a href="ISpy?ac=Q94741,P35360">View examples</a>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>References</td>
-<td class=inf valign=top width=1200><ol>
-<li value=1><a name=PUB00005667>
-Watson S., Arkinstall S.<br>
-<i>Opsins.</i><br>
-In: The G-protein Linked Receptor Factsbook. Academic Press, London, 1994, pp.214-222. [ISBN 0127384405]
-[PUB00005667]
-
-<li value=2><a name=PUB00004821>
-Smith W.C., Price D.A., Greenberg R.M., Battelle B.A.<br>
-<i>Opsins from the lateral eyes and ocelli of the horseshoe crab, Limulus polyphemus.</i><br>
-Proc. Natl. Acad. Sci. U.S.A. 90: 6150-6154(1993).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=93317641&form=6&db=m&Dopt=b">[MEDLINE:93317641]</a>
-[PUB00004821]
-</ol></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=matches", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Matches
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><a href="ISpy?ipr=IPR001391&display=n">Table</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001391&display=n&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001391">Graphical</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001391&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="http://www.ebi.ac.uk/~flo/cgi-bin/InterPro_GUI/script/ReqInterPro.pl?list_ipr_ac=IPR001391">Condensed graphical view</a></td></tr>
-
-</table></td></tr></table>
View
64 Tests/InterPro/IPR001442.htm
@@ -1,64 +0,0 @@
-<!doctype html public "-//W3C//DTD HTML 4.0//EN">
-<html><head>
-<link rel="stylesheet" href="ipa_styles.css" type="text/css">
-<title>InterPro Entry IPR001442</title></head>
-<body bgcolor=white>
-<a border=0 href="index.html">
-<img border=0 src="images/interpro_logo.jpeg"></a>
-<table width=600 class=frame border=0><tr><td><table border=0 width=100% cellspacing=1 cellpadding=3><tr><td class=tag>InterPro Entry IPR001442</td></tr></table></td></tr></table>
-<h2 class=name>C-terminal tandem repeated domain in type 4 procollagen</h2>
-<table class=frame border=0 width="100%"><tr><td>
-<table border=0 cellspacing=1 cellpadding=3 width=100%>
-<tr>
-<td class=tag valign=top width=110>Database</td>
-<td class=inf valign=top width=1200>InterPro</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Accession</td>
-<td class=inf valign=top width=1200>IPR001442; C4 (matches 61 proteins)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Name</td>
-<td class=inf valign=top width=1200>C-terminal tandem repeated domain in type 4 procollagen</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Type</td>
-<td class=inf valign=top width=1200><A href="#" onClick='w=window.open("IHelpServlet?help=Repeat", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Repeat
-<img src="gifs/help.gif" width=19 height=19 border=0 alt=""></a></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Dates</td>
-<td class=inf valign=top width=1200>08-OCT-1999 (created)<BR>29-FEB-2000 (last modified)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Signatures</td>
-<td class=inf valign=top width=1200>
-<a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF01413">PF01413</a>; C4
- (60 proteins)<br><a href="http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD003923">PD003923</a>; C4
- (60 proteins)<br><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=C4&BLAST=DUMMY">SM00111</a>; C4
- (61 proteins)<br></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=abstract", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Abstract
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>This duplicated domain is present at the C-terminus of type 4 collagen, the major structural component of glomerular basement membranes (GMB) forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Examples</td>
-<td class=inf valign=top width=1200><ul>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P53420]">P53420</a> CA44_HUMAN</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P27393]">P27393</a> CA24_ASCSU</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:Q28247]">Q28247</a> CA54_CANFA</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P08120]">P08120</a> CA14_DROME</li>
-<br><a href="ISpy?ac=P53420,P27393,Q28247,P08120">View examples</a>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=matches", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Matches
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><a href="ISpy?ipr=IPR001442&display=n">Table</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001442&display=n&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001442">Graphical</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001442&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="http://www.ebi.ac.uk/~flo/cgi-bin/InterPro_GUI/script/ReqInterPro.pl?list_ipr_ac=IPR001442">Condensed graphical view</a></td></tr>
-
-</table></td></tr></table>
View
152 Tests/InterPro/IPR001571.htm
@@ -1,152 +0,0 @@
-<!doctype html public "-//W3C//DTD HTML 4.0//EN">
-<html><head>
-<link rel="stylesheet" href="ipa_styles.css" type="text/css">
-<title>InterPro Entry IPR001571</title></head>
-<body bgcolor=white>
-<a border=0 href="index.html">
-<img border=0 src="images/interpro_logo.jpeg"></a>
-<table width=600 class=frame border=0><tr><td><table border=0 width=100% cellspacing=1 cellpadding=3><tr><td class=tag>InterPro Entry IPR001571</td></tr></table></td></tr></table>
-<h2 class=name>Vasoactive intestinal peptide receptor</h2>
-<table class=frame border=0 width="100%"><tr><td>
-<table border=0 cellspacing=1 cellpadding=3 width=100%>
-<tr>
-<td class=tag valign=top width=110>Database</td>
-<td class=inf valign=top width=1200>InterPro</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Accession</td>
-<td class=inf valign=top width=1200>IPR001571; Vasoactintest_receptor (matches 11 proteins)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Name</td>
-<td class=inf valign=top width=1200>Vasoactive intestinal peptide receptor</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Type</td>
-<td class=inf valign=top width=1200><A href="#" onClick='w=window.open("IHelpServlet?help=Family", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Family
-<img src="gifs/help.gif" width=19 height=19 border=0 alt=""></a></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Dates</td>
-<td class=inf valign=top width=1200>08-OCT-1999 (created)<BR>09-MAR-2000 (last modified)</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Signatures</td>
-<td class=inf valign=top width=1200>
-<a href="http://methionine.sbc.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=PR00491">PR00491</a>; VASOACTVEIPR
- (11 proteins)<br></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=parent", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Parent
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a><br><a href="ITreeDisplay?ipr=IPR001571">[tree]</a></td><td class=inf valign=top width=1200>
-<a href="/interpro/IEntry?ac=IPR000832">IPR000832</a>; G-protein coupled receptors family 2 (secretin-like) (388 proteins)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=children", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Children
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a><br><a href="ITreeDisplay?ipr=IPR001571">[tree]</a></td><td class=inf valign=top width=1200>
-<a href="/interpro/IEntry?ac=IPR001771">IPR001771</a>; Vasoactive intestinal peptide receptor 1 (15 proteins)<br>
-<a href="/interpro/IEntry?ac=IPR002284">IPR002284</a>; Vasoactive intestinal peptide receptor 2 (3 proteins)<br>
-<a href="/interpro/IEntry?ac=IPR002285">IPR002285</a>; Pituitary adenylate cyclase activating polypeptide type 1 receptor (9 proteins)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=molecularfunction", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Function
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>vasoactive intestinal peptide receptor (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0004999">GO:0004999</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=cellularcomponent", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Component
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>membrane (<a href="http://www.informatics.jax.org/go/GO.cgi?id=GO:0016020">GO:0016020</a>)<br>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=abstract", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Abstract
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200>
-<!-- common_annotation id=AB00003 -->
-<p>G-protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence [1]. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family.</p>
-<!-- /common_annotation id=AB00003 -->
-
-
-<!-- common_annotation id=AB00007 -->
-<p>The secretin-like GPCRs include secretin [2], calcitonin [3], parathyroid hormone/parathyroid hormone-related peptides [4] and vasoactive intestinal peptide [5], all of which activate adenylyl cyclase and the phosphatidyl-inositol-calcium pathway. The amino acid sequences of the receptors contain high proportions of hydrophobic residues grouped into 7 domains, in a manner reminiscent of the rhodopsins and other receptors believed to interact with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence identity between these families: the secretin-like receptors thus bear their own unique '7TM' signature.</p>
-<!-- /common_annotation id=AB00007 -->
-
-<p>Vasoactive intestinal polypeptide (VIP) has a wide physiological profile.
-In the periphery, it induces relaxation in smooth muscle; inhibits
-secretion in certain tissues, but stimulates secretion in others; and
-modulates activity of cells in the immune system [6]. In the CNS, it has a
-range of both excitatory and inhibitory actions. VIP receptors are
-distributed widely in the periphery, and occur throughout the gastrointestinal tract and genitourinary system, other smooth muscles and
-secretory glands. In the CNS, they are found abundantly in, e.g. the cortex,
-hippocampus and thalamus [6]. All VIP receptors activate adenylyl cyclase.</p></td></tr>
-
-<tr>
-<td class=tag valign=top width=110>Examples</td>
-<td class=inf valign=top width=1200><ul>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P32241]">P32241</a> VIPR_HUMAN</li>
-<li><a href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-newId+-e+[SWall-ACC:P41588]">P41588</a> VIPS_MOUSE</li>
-<br><a href="ISpy?ac=P32241,P41588">View examples</a>
-</td></tr>
-
-<tr>
-<td class=tag valign=top width=110>References</td>
-<td class=inf valign=top width=1200><ol>
-<li value=1><a name=PUB00004961>
-Attwood T.K., Findlay J.B.C.<br>
-<i>Fingerprinting G-protein-coupled receptors.</i><br>
-Protein Eng. 7: 195-203(1994).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=94224751&form=6&db=m&Dopt=b">[MEDLINE:94224751]</a>
-[PUB00004961]
-
-<li value=2><a name=PUB00001208>
-Ishihara T., Nakamura S., Kaziro Y., Takahashi T., Takahashi K., Nagata S.<br>
-<i>Molecular cloning and expression of a cDNA encoding the secretin receptor.</i><br>
-EMBO J. 10: 1635-1641(1991).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=91266890&form=6&db=m&Dopt=b">[MEDLINE:91266890]</a>
-[PUB00001208]
-
-<li value=3><a name=PUB00005147>
-Lin H.Y., Harris T.L., Flannery M.S., Aruffo A., Kaji E.H., Gorn A., Kolakowski L.F., Lodish H.F., Goldring S.R.<br>
-<i>Expression cloning of adenylate cyclase-coupled calcitonin receptor.</i><br>
-Science 254: 1022-1024(1991).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=92054591&form=6&db=m&Dopt=b">[MEDLINE:92054591]</a>
-[PUB00005147]
-
-<li value=4><a name=PUB00005148>
-Jueppner H., Abou-Samra A.-B., Freeman M., Kong X.-F., Schipani E., Richards J., Kolakowski L.F.Jr., Hock J., Potts J.T.Jr., Kronenberg H.M., Segre G.V.<br>
-<i>A G-protein linked receptor for parathyroid hormone and parathyroid hormone-related peptide.</i><br>
-Science 254: 1024-1026(1991).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=92054592&form=6&db=m&Dopt=b">[MEDLINE:92054592]</a>
-[PUB00005148]
-
-<li value=5><a name=PUB00004310>
-Ishihara T., Shigemoto R., Mori K., Takahashi K., Nagata S.<br>
-<i>Functional expression and tissue distribution of a novel receptor for vasoactive intestinal polypeptide.</i><br>
-Neuron 8: 811-819(1992).
-<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=92232309&form=6&db=m&Dopt=b">[MEDLINE:92232309]</a>
-[PUB00004310]
-
-<li value=6><a name=PUB00005907>
-Watson S., Arkinstall S.<br>
-<i>Vasoactive intestinal polypeptide family.</i><br>
-In: The G-protein Linked Receptor Factsbook. Academic Press, London, 1994, pp.278-283. [ISBN 0127384405]
-[PUB00005907]
-</ol></td></tr>
-
-<tr>
-<td class=tag valign=top width=110><A href="#" onClick='w=window.open("IHelpServlet?help=matches", "helpwindow", "width=450,height=400,scrollbars=yes,resizable=yes");w.focus();'>
-Matches
-<img src="gifs/helptag.gif" width=19 height=19 border=0 alt=""></a></td>
-<td class=inf valign=top width=1200><a href="ISpy?ipr=IPR001571&display=n">Table</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001571&display=n&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001571">Graphical</a>&nbsp;&nbsp;&nbsp;<a href="ISpy?ipr=IPR001571&dmax=20000">all</a>&nbsp;&nbsp;&nbsp;<a href="http://www.ebi.ac.uk/~flo/cgi-bin/InterPro_GUI/script/ReqInterPro.pl?list_ipr_ac=IPR001571">Condensed graphical view</a></td></tr>
-
-</table></td></tr></table>
View
238 Tests/output/test_interpro
@@ -1,238 +0,0 @@
-test_interpro
-
-Abstract
-Crystallins are the dominant structural components of the eye lens. Among the di...
-Accession: IPR001064; Crystallin (matches 132 proteins)
-Component:
-Database: InterPro
-
-Database links
-PROSITE doc;PDOC00197
-Blocks;IPB001064
-Dates: 08-OCT-1999 (created)05-DEC-2000 (last modified)
-
-Examples
-P02966DESS_MYXXA: A calcium-binding protein from the sporulating bacterium Myxococcus xanthusa forms a major part of the spore coat
-P46058EDSP_CYNPY
-P09353SR3A_PHYPO: Spherulin 3a from the slime mold Physarum polycephalum. Spherulin 3a is a development specific protein synthesized in response to various kinds of stress leading to encystment and dormancy. The sequence of Spherulin 3a consists of two 'Greek key' motifs [3]
-P06504CRBS_BOVIN
-Q91314CB12_RANCA
-P07317CRBA_RANTE
-Function:
-Name: Crystallin
-Parent:
-Process:
-
-References
-authors: Wistow G.J., Piatigorsky J.
-title: Lens crystallins: the evolution and expression of proteins for a highly specialized tissue.
-journal: Annu. Rev. Biochem. 57: 479-504(1988).
-medline id: 89024580
-pubmed id: PUB00000056
-comment:
-
-authors: Lubsen N.H., Aarts H.J.M., Schoenmakers J.G.G.
-title: The evolution of lenticular proteins: the beta- and gamma-crystallin super gene family.
-journal: Prog. Biophys. Mol. Biol. 51: 47-76(1988).
-medline id: 89113769
-pubmed id: PUB00004933
-comment:
-
-authors: Wistow G.
-title: Evolution of a protein superfamily: relationships between vertebrate lens crystallins and microorganism dormancy proteins.
-journal: J. Mol. Evol. 30: 140-145(1990).
-medline id: 90189184
-pubmed id: PUB00003409
-comment:
-
-
-
-Signatures
-PS00225; CRYSTALLIN_BETAGAMMA (1586 proteins)
-PR01367; BGCRYSTALLIN (102 proteins)
-PF00030; crystall (113 proteins)
-SM00247; XTALbg (129 proteins)
-Type: Domain
-
-
-
-
-Abstract
-The twofungalenzymes, C-14 sterol reductase (gene ERG24 inbudding yeastand erg3 ...
-Accession: IPR001171; ERG4_ERG24 (matches 29 proteins)
-Component: membrane (GO:0016020)
-Database: InterPro
-
-Database links
-PROSITE doc;PDOC00780
-Blocks;IPB001171
-Dates: 08-OCT-1999 (created)14-NOV-2000 (last modified)
-
-Examples
-P38670ER24_NEUCR
-P23913LBR_CHICK
-P36209STS1_SCHPO
-Function:
-Name: Ergosterol biosynthesis ERG4/ERG24 enzymes
-Parent:
-Process:
-
-References
-authors: Lai M.H., Bard M., Pierson C.A., Alexander J.F., Goebl M., Carter G.T., Kirsch D.R.
-title: The identification of a gene family in the Saccharomyces cerevisiae ergosterol biosynthesis pathway.
-journal: Gene 140: 41-49(1994).
-medline id: 94171077
-pubmed id: PUB00001844
-comment:
-
-
-
-Signatures
-PS01017; ERG4_ERG24_1 (16 proteins)
-PS01018; ERG4_ERG24_2 (13 proteins)
-PF01222; ERG4_ERG24 (29 proteins)
-Type: Family
-
-
-
-
-Abstract
-Opsins are the photoreceptors ofanimalretinas [1]:vertebraterhodopsin is found i...
-Accession: IPR001391; Opsin_lateye (matches 23 proteins)
-Component: membrane (GO:0016020)
-Database: InterPro
-
-Database links
-Dates: 08-OCT-1999 (created)27-NOV-2000 (last modified)
-
-Examples
-Q94741OPS1_SCHGR
-P35360OPS1_LIMPO
-Function: G-protein coupled receptor (GO:0004930)
-Name: Lateral eye opsin
-Parent:
-Process: phototransduction (GO:0007602)
-
-References
-authors: Watson S., Arkinstall S.
-title: Opsins.
-journal:
-medline id:
-pubmed id: PUB00005667
-comment:
-
-authors: Smith W.C., Price D.A., Greenberg R.M., Battelle B.A.
-title: Opsins from the lateral eyes and ocelli of the horseshoe crab, Limulus polyphemus.
-journal: Proc. Natl. Acad. Sci. U.S.A. 90: 6150-6154(1993).
-medline id: 93317641
-pubmed id: PUB00004821
-comment:
-
-
-
-Signatures
-PR00578; OPSINLTRLEYE (23 proteins)
-Type: Family
-
-
-
-
-Abstract
-This duplicated domain is present at the C-terminus of type 4 collagen, the maj...
-Accession: IPR001442; C4 (matches 61 proteins)
-Component:
-Database: InterPro
-
-Database links
-Dates: 08-OCT-1999 (created)29-FEB-2000 (last modified)
-
-Examples
-P53420CA44_HUMAN
-P27393CA24_ASCSU
-Q28247CA54_CANFA
-P08120CA14_DROME
-Function:
-Name: C-terminal tandem repeated domain in type 4 procollagen
-Parent:
-Process:
-
-References
-
-
-Signatures
-PF01413; C4 (60 proteins)
-PD003923; C4 (60 proteins)
-SM00111; C4 (61 proteins)
-Type: Repeat
-
-
-
-
-Abstract
-G-protein-coupled receptors (GPCRs) constitute a vast protein family that encomp...
-Accession: IPR001571; Vasoactintest_receptor (matches 11 proteins)
-Component: membrane (GO:0016020)
-Database: InterPro
-
-Database links
-Dates: 08-OCT-1999 (created)09-MAR-2000 (last modified)
-
-Examples
-P32241VIPR_HUMAN
-P41588VIPS_MOUSE
-Function: vasoactive intestinal peptide receptor (GO:0004999)
-Name: Vasoactive intestinal peptide receptor
-Parent:
-Process:
-
-References
-authors: Attwood T.K., Findlay J.B.C.
-title: Fingerprinting G-protein-coupled receptors.
-journal: Protein Eng. 7: 195-203(1994).
-medline id: 94224751
-pubmed id: PUB00004961
-comment:
-
-authors: Ishihara T., Nakamura S., Kaziro Y., Takahashi T., Takahashi K., Nagata S.
-title: Molecular cloning and expression of a cDNA encoding the secretin receptor.
-journal: EMBO J. 10: 1635-1641(1991).
-medline id: 91266890
-pubmed id: PUB00001208
-comment:
-
-authors: Lin H.Y., Harris T.L., Flannery M.S., Aruffo A., Kaji E.H., Gorn A., Kolakowski L.F., Lodish H.F., Goldring S.R.
-title: Expression cloning of adenylate cyclase-coupled calcitonin receptor.
-journal: Science 254: 1022-1024(1991).
-medline id: 92054591
-pubmed id: PUB00005147
-comment:
-
-authors: Jueppner H., Abou-Samra A.-B., Freeman M., Kong X.-F., Schipani E., Richards J., Kolakowski L.F.Jr., Hock J., Potts J.T.Jr., Kronenberg H.M., Segre G.V.
-title: A G-protein linked receptor for parathyroid hormone and parathyroid hormone-related peptide.
-journal: Science 254: 1024-1026(1991).
-medline id: 92054592
-pubmed id: PUB00005148
-comment:
-
-authors: Ishihara T., Shigemoto R., Mori K., Takahashi K., Nagata S.
-title: Functional expression and tissue distribution of a novel receptor for vasoactive intestinal polypeptide.
-journal: Neuron 8: 811-819(1992).
-medline id: 92232309
-pubmed id: PUB00004310
-comment:
-
-authors: Watson S., Arkinstall S.
-title: Vasoactive intestinal polypeptide family.
-journal:
-medline id:
-pubmed id: PUB00005907
-comment:
-
-
-
-Signatures
-PR00491; VASOACTVEIPR (11 proteins)
-Type: Family
-
-
-
View
29 Tests/test_interpro.py
@@ -1,29 +0,0 @@
-# Copyright 2001 by Katharine Lindner. All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license. Please see the LICENSE file that should have been included
-# as part of this package.
-
-#!/usr/bin/env python
-"""Test the InterPro parser and make sure everything is working smoothly.
-"""
-# standard library
-import os
-
-# Biopython
-from Bio import InterPro
-
-test_files = ['IPR001064.htm', 'IPR001171.htm', 'IPR001391.htm',
- 'IPR001442.htm', 'IPR001571.htm']
-
-
-
-# test the parser
-record_parser = InterPro.InterProParser()
-
-for test in test_files:
- datafile = os.path.join( 'InterPro', test )
- src_handle = open( datafile )
- data = record_parser.parse( src_handle )
- print data
- print '\n'
-
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