This information is over 2 years old. Information was current at time of publication.{"id":181,"date":"2013-03-14T13:31:36","date_gmt":"2013-03-14T18:31:36","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=181"},"modified":"2013-03-14T13:31:36","modified_gmt":"2013-03-14T18:31:36","slug":"workshop-3202013","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2013\/03\/14\/workshop-3202013\/","title":{"rendered":"Workshop 3\/20\/2013"},"content":{"rendered":"<p><strong><span style=\"color: red;font-size: medium\"><big>Sequence Similarity Searching<\/big><\/span><\/strong><br \/>\n<strong><span style=\"font-size: medium\">by Ansuman Chattopadhyay, PhD<br \/>\n<\/span><\/strong><br \/>\n<strong><span style=\"color: #33cc00;font-size: medium\">Wednesday, 20th March 2013<br \/>\n1-3 pm<br \/>\nFalk Library Classroom 2 (upstairs)<\/span><\/strong><\/p>\n<p>Registration is NOT required.<\/p>\n<p>This workshop will introduce a variety of databases and tools, including:<\/p>\n<ul>\n<li><strong>NCBI BLAST<\/strong>: set up and perform a search, decipher the output, analyze the results<\/li>\n<li><strong>NCBI PSI-BLAST<\/strong>: used to identify wear\/subtle homologies to annotated entries in the NCBI Entrez Protein database (<strong>P<\/strong>osition <strong>S<\/strong>pecific <strong>I<\/strong>terated)<\/li>\n<li><strong>BLink<\/strong>: displays the results of BLAST searches that have been done for every protein sequence in the Entrez Protein database<\/li>\n<li><strong>EMBL-EBI<\/strong>: the European equivalent of NCBI, offering more sequence similarity searching tools\n<ul>\n<li><span style=\"text-decoration: underline\">Fasta<\/span>: used for a fast protein comparison or a fast nucleotide comparison<\/li>\n<li><span style=\"text-decoration: underline\">MPsrch<\/span>: a biological sequence comparison tool<\/li>\n<li><span style=\"text-decoration: underline\">ScanPS<\/span>: a program for comparing a protein sequence to a database of protein sequences<\/li>\n<\/ul>\n<\/li>\n<li><strong>UCSC BLAT<\/strong>: a tool which performs rapid mRNA\/DNA and protein alignments<\/li>\n<\/ul>\n<p>Participants will learn how to answer questions like:<\/p>\n<ul>\n<li>Are there any sequences homologous to my sequence of interest?<\/li>\n<li>How do I determine the percent identity of two sequences?<\/li>\n<li>What is the domain architecture for my protein of interest?<\/li>\n<li>Are there any proteins that have similar domain architecture to my protein of interest?<\/li>\n<\/ul>\n<p>This class is approved for AMA Category 2 CME credit.<\/p>\n<p><a href=\"http:\/\/files.hsls.pitt.edu\/files\/molbio\/MolbioWorkshops.pdf\">HSLS Winter\/Spring 2013 Bioinformatics Training Workshops schedule<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p><strong><span style=\"color: red;font-size: medium\">Sequence Similarity Searching<\/span><\/strong><br \/>\n<strong><span style=\"font-size: medium\">by Ansuman Chattopadhyay, PhD<br \/>\n<\/span><\/strong><br \/>\n<strong><span style=\"color: #33cc00;font-size: medium\">Wednesday, 20th March 2013<br \/>\n1-3 pm<br \/>\nFalk Library Classroom 2 (upstairs)<\/span><\/strong><\/p>\n<p>Registration is NOT required.<\/p>\n<p><a class=\"read-more\" alt= \"Workshop 3\/20\/2013\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2013\/03\/14\/workshop-3202013\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[13],"tags":[],"class_list":["post-181","post","type-post","status-publish","format-standard","hentry","category-workshops"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/181","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/31"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=181"}],"version-history":[{"count":7,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/181\/revisions"}],"predecessor-version":[{"id":188,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/181\/revisions\/188"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=181"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=181"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=181"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}