{"id":132,"date":"2014-11-10T23:22:12","date_gmt":"2014-11-10T23:22:12","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=132"},"modified":"2015-06-27T20:57:18","modified_gmt":"2015-06-27T20:57:18","slug":"pb-align-sequence","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=132","title":{"rendered":"seqPB-ALIGNm"},"content":{"rendered":"<p><!--more--><\/p>\n<h2>Very fast and efficient structure comparison and mining using protein blocks<\/h2>\n<table class=\"table1\" style=\"width: 100%;\">\n<tbody>\n<tr>\n<td class=\"column1\" style=\"text-align: left;\">\n<h2>seqPB-ALIGNm<\/h2>\n<p><strong>seqPB-ALIGNm is a structure mining tool.<\/strong> It compares a <strong>query PB sequence<\/strong> with all structural domains in SCOP and finds structures that have similar fold to the query. It then performs local (Smith Waterman) or global (Needleman-Wunsch) alignment with every structural domains available in SCOP 1.75. SCOP domains that share local or global structural similarities with the query are extracted PB-ALIGNc. seqPB-ALIGNm is fast and takes about 1 min to search for database.<\/p>\n<form action=\"\/cgi-bin\/PBE\/pb2all.cgi\" enctype=\"multipart\/form-data\" method=\"post\">\n<div style=\"text-align: left;\"><span class=\"para\"><a name=\"QUERY HERE\"><\/a><big style=\"font-weight: bold;\">seqPB-ALIGNm<\/big> (PB sequence against\u00a0database )<\/span> <span class=\"para\"> <\/span><\/div>\n<p><span class=\"highlight\">Paste your PB sequence here<\/span><span class=\"para\"><span style=\"color: rgb(204, 204, 255);\"> &nbsp;&nbsp;<\/span><textarea cols=\"60\" rows=\"2\" name=\"pbsequence\"><\/textarea>&nbsp;<\/span><\/p>\n<p><span class=\"highlight\">Select SCOP class<\/span><\/p>\n<p><select name=\"class\"><option selected=\"selected\" value=\".\"> All <\/option><option value=\"a\">Alpha<\/option><option value=\"b\">Beta<\/option><option value=\"c\">AB<\/option><option value=\"d\">AplusB<\/option><option value=\"e\">Multido<\/option><option value=\"f\">Membrane<\/option><option value=\"g\">Small<\/option><\/select><\/p>\n<p><span class=\"highlight\">Length (in %)<input name=\"length\" type=\"text\" value=\"30\" \/><\/span><\/p>\n<p><span class=\"highlight\">Ranks<input name=\"top\" value=\"20\" \/><\/span><span class=\"highlight\"> [input number of top alignments in results you would like to see<\/span><\/p>\n<p><input checked=\"checked\" name=\"alignment\" type=\"radio\" value=\"LOCAL\" \/><span class=\"highlight\">Local alignment <\/span><\/p>\n<p><input name=\"alignment\" type=\"radio\" value=\"GLOBAL\" \/><span class=\"highlight\">Global alignment<\/span><\/p>\n<p><input name=\"submit\" type=\"submit\" value=\"Go\" \/> <small style=\"font-weight: bold;\"><\/p>\n<\/form>\n<form action=\"\/cgi-bin\/PBE\/one2all_result.cgi\" method=\"post\">\n<hr style=\"height: 4px; width: 100%;\" \/><span class=\"highlight\"><span style=\"color: #000000;\">To obtain the results of\u00a0already done query, input the assigned JOBID : <\/span><br \/>\n<input name=\"jobid\" \/><\/span><br \/>\n<input name=\"submit\" type=\"submit\" value=\"results\" \/> <\/form>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>PB-ALIGN group<\/h3>\n<address>Swapnil Mahajan, Manoj Tyagi, Priyanka Sharma, Fr\u00e9d\u00e9ric Cadet, N. Srinivasan, Alexandre G. de Brevern &amp; Bernard Offmann<\/address>\n<address>Site maintained by :S. Mahajan, P. Sharma, M. Tyagi and B. Offmann<\/address>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"page-without-sidebar.php","meta":{"footnotes":""},"class_list":["post-132","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/132","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=132"}],"version-history":[{"count":9,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/132\/revisions"}],"predecessor-version":[{"id":142,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/132\/revisions\/142"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=132"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}