{"id":110,"date":"2012-02-16T13:16:17","date_gmt":"2012-02-16T13:16:17","guid":{"rendered":"http:\/\/.\/?page_id=110"},"modified":"2015-06-03T00:16:11","modified_gmt":"2015-06-03T00:16:11","slug":"pb-svindex-help","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/?page_id=110","title":{"rendered":"PB-SVindex Help"},"content":{"rendered":"<div class=\"post-meta\">Last update on Wednesday, June 3, 2015<\/div><h2><a href=\".\/?page_id=12\" title=\"PB-SVindex\">PB-SV<em>index<\/em><\/a><\/h2>\n<p><strong><em>PB-SVindex : knowledge-based calculation of Structural Variability Indices of pentapeptide sequences<\/em><\/strong><\/p>\n<p>This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from <a href=\".\/?page_id=4\">PB-PENTAdb<\/a> database to calculate structural variability index (SVI) for each of them. It is a statistical index that shows if a pentapeptide is observed to have multiple local conformations in terms of PBs or not.<\/p>\n<p>This proposed index is similar to the <strong>Simpson&#8217;s diversity index<\/strong> used in population genetics :<\/p>\n<p><a href=\".\/wp-content\/uploads\/2010\/08\/simpson-index.png\"><img decoding=\"async\" class=\"alignnone size-full wp-image-981\" title=\"simpson index\" src=\".\/wp-content\/uploads\/2010\/08\/simpson-index.png\" alt=\"\" \/><\/a><\/p>\n<p><em>pi<\/em> is the fraction of all organisms which belong to the <em>i<\/em>-th species<\/p>\n<p>Here we calculate SVI using an approximation of Simpson&#8217;s index :<\/p>\n<p><a href=\".\/wp-content\/uploads\/2010\/08\/simpson-3.png\"><img loading=\"lazy\" decoding=\"async\" src=\".\/wp-content\/uploads\/2010\/08\/simpson-3.png\" alt=\"\" title=\"simpson 3\" width=\"150\" height=\"60\" class=\"alignnone size-full wp-image-1009\" \/><\/a><\/p>\n<p>where, for a given amino acid motif, <em>ni<\/em> is its occurence in PB class <em>i<\/em>, and <em>n<\/em> is the total number of times this motif is found in the database.<br \/>\nThis is an estimator for Simpson&#8217;s index for sampling without replacement.<\/p>\n<p>Assigned variability index values vary between 0 and 1. <strong>Lower values<\/strong> indicate sequences with <strong>low structural variability<\/strong>, <strong>higher values<\/strong> indicate <strong>higher structural variability<\/strong>.<\/p>\n<p>\nUser can provide a SCOP domain ID to get the SVindex values for its sequence.<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/svi_domain.png\" target=\"_blank\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/svi_domain.png\" alt=\"SVindex SCOP Domain ID Input\" \/><\/a><br \/>\n<br \/>\nThe output of this query will give a result page as follows<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/svi_domain_result.png\" target=\"_blank\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/svi_domain_result.png\" alt=\"SVindex Domain Result\" \/><\/a><br \/>\n\n<\/p>\n<p>\nUser can choose to provide one more protein sequences in fasta format (1000 sequences at most) as shown below<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/svi_seq.png\" target=\"_blank\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/svi_seq.png\" alt=\"SVindex Sequence Query\" \/><\/a><br \/>\n<br \/>\nAs output, a table is provided with<\/p>\n<ul>\n<li>first 8 characters of ID of sequence (it removes the &#8220;>&#8221; from first line)<\/li>\n<li>Number of residues in sequence<\/li>\n<li>SV index<\/li>\n<\/ul>\n<p>with SVindices values separated by comas.<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/svi_seq_result.png\" target=\"_blank\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/svi_seq_result.png\" alt=\"SVindex Sequence Query\" \/><\/a><br \/>\n<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Last update on Wednesday, June 3, 2015PB-SVindex PB-SVindex : knowledge-based calculation of Structural Variability Indices of pentapeptide sequences This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from PB-PENTAdb database to calculate structural variability index &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"more-link\" href=\"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/?page_id=110\"> <span class=\"screen-reader-text\">PB-SVindex Help<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":49,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"full-width-page.php","meta":{"footnotes":""},"class_list":["post-110","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/110","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=110"}],"version-history":[{"count":13,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/110\/revisions"}],"predecessor-version":[{"id":380,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/110\/revisions\/380"}],"up":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/49"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=110"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}