{"id":413,"date":"2013-04-26T13:59:06","date_gmt":"2013-04-26T13:59:06","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=413"},"modified":"2019-05-15T11:03:25","modified_gmt":"2019-05-15T11:03:25","slug":"blast","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/blast\/","title":{"rendered":"BLAST"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.<\/p>\n<p>Two pre-compiled binary versions are available on the CSF:<\/p>\n<ul>\n<li>BLAST+ &#8211; a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. Versions 2.3.0 and 2.2.30 and 2.2.27 are available.<\/li>\n<li>BLAST (legacy) 2.2.26 &#8211; blastall, blastpgp, etc<\/li>\n<\/ul>\n<p>For further information about the differences:<\/p>\n<ul>\n<li><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?CMD=Web&#038;PAGE_TYPE=BlastDocs&#038;DOC_TYPE=Download\">BLAST Download Site<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK62345\/\">BLAST FTP Site book<\/a><\/li>\n<\/ul>\n<h2>Restrictions on use<\/h2>\n<p>The software is public domain and available to all users. For further info load the BLAST+ modulefile and consult <code>$BLASTP_HOME\/LICENSE<\/code><\/p>\n<h2>Set up procedure<\/h2>\n<p>For BLAST+ load <em>one<\/em> of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/binapps\/blast\/blast+\/2.4.0\r\nmodule load apps\/binapps\/blast\/blast+\/2.3.0\r\nmodule load apps\/binapps\/blast\/blast+\/2.2.30\r\nmodule load apps\/binapps\/blast\/blast+\/2.2.27\r\n<\/pre>\n<p>and for BLAST (legacy):<\/p>\n<pre>\r\nmodule load apps\/binapps\/blast\/legacy\/2.2.26\r\n<\/pre>\n<p>If you have your <em>own<\/em> set of databases you will need a <code>.ncbirc<\/code> file in your home directory which tells BLAST where to find them. For example:<\/p>\n<pre class=\"in1\">\r\n[BLAST]\r\nBLASTDB=$HOME\/genome_analysis\/Blast\/data\r\n               #\r\n               # The the correct path for where ever you store your own databases\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run BLAST on the login node. All work must be submitted to batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the relevant modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n\r\nblastx -db efungi_pep_no_afua -query auto_351\/contigs.fa -num_threads $NSLOTS -out 351un.out \\\r\n       -evalue 1e-20 -max_target_seqs 1 -outfmt 6\r\n<\/pre>\n<p>Submit the job using:<\/p>\n<pre>qsub <em>script<\/em><\/pre>\n<p>where <code><em>script<\/em><\/code> is the name of your jobscript file.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Make sure you have the relevant modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n#$ -pe smp.pe 4 \r\n\r\nblastx -db efungi_pep_no_afua -query auto_351\/contigs.fa -num_threads $NSLOTS -out 351un.out \\\r\n       -evalue 1e-20 -max_target_seqs 1 -outfmt 6\r\n<\/pre>\n<p>Submit the job using:<\/p>\n<pre>qsub <em>script<\/em><\/pre>\n<p>where <code><em>script<\/em><\/code> is the name of your jobscript file.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\/\">BLAST homepage at NCBI<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Two pre-compiled binary versions are available on the CSF: BLAST+ &#8211; a new suite of BLAST tools that utilizes the NCBI C++.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/blast\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-413","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/413","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=413"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/413\/revisions"}],"predecessor-version":[{"id":4983,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/413\/revisions\/4983"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=413"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}