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
Two pre-compiled binary versions are available on the CSF:<\/p>\n
For further information about the differences:<\/p>\n
The software is public domain and available to all users. For further info load the BLAST+ modulefile and consult For BLAST+ load the following modulefiles:<\/p>\n and for BLAST (legacy):<\/p>\n If you have your own<\/em> set of databases you will need a We have downloaded the following FASTA database files from the NCBI BLAST repository:<\/p>\n We have downloaded the following BLAST pre-formatted databases from the NCBI BLAST repository:<\/p>\n The The intention is to save users some RDS space by having a central copy of some of the databases, where we have received more than one request for the same DB.<\/p>\n Please do not run BLAST on the login node. All work must be submitted to batch.<\/p>\n Make sure you have the relevant modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the job using:<\/p>\n where Make sure you have the relevant modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the job using:<\/p>\n where 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+ – a new suite of BLAST tools that utilizes the NCBI C++.. Read more »<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3286","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3286","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=3286"}],"version-history":[{"count":9,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3286\/revisions"}],"predecessor-version":[{"id":11923,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3286\/revisions\/11923"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=3286"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}$BLASTP_HOME\/LICENSE<\/code><\/p>\nSet up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/blast@2.17.0\r\nmodule load apps\/binapps\/blast\/2.13.0 # Load apps\/gcc\/perl\/5.34.0 for you\r\nmodule load apps\/binapps\/blast\/2.9.0\r\nmodule load apps\/binapps\/blast\/2.4.0\r\n\r\n# You should also load the following if downloading data, e.g., using update_blastdb.pl\r\nmodule load tools\/env\/proxy\r\n<\/pre>\n
\r\nmodule load apps\/binapps\/blast\/legacy\/2.2.26\r\n<\/pre>\n
.ncbirc<\/code> file in your home directory which tells BLAST where to find them. For example:<\/p>\n\r\n[BLAST]\r\nBLASTDB=$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
NCBI BLAST Databases<\/h2>\n
\r\n# Download using:\r\n# wget -N --continue --directory-prefix FASTA ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/db\/v5\/FASTA\/nr.gz\r\n# Then gunzip'd after checking the md5sum of the download.\r\nFASTA\/nr\r\nFASTA\/nt\r\nFASTA\/pdbaa\r\nFASTA\/swissport\r\n<\/pre>\n
\r\n# Downloaded using:\r\n# update_blastdb.pl --source aws --decompress --num_threads $NSLOTS DBNAME<\/em>\r\nnr # See nr.NN<\/em>.*\r\nnt # See nt.NN<\/em>.*\r\n<\/pre>\n
2.13.0<\/code> modulefile (see above) will set the following env var to point to the location of the files:<\/p>\n\r\nNCBI_BLAST_DIR=\/mnt\/data-sets\/ncbi\/blast\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd\r\nmodule load apps\/binapps\/blast\/2.13.0\r\n\r\nblastx -db efungi_pep_no_afua -query auto_351\/contigs.fa -num_threads $NSLOTS -out 351un.out \\\r\n -evalue 1e-20 -max_target_seqs 1 -outfmt 6\r\n<\/pre>\n
qsub script<\/em><\/pre>\n
script<\/em><\/code> is the name of your jobscript file.<\/p>\nParallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 4 \r\nmodule load apps\/binapps\/blast\/2.13.0\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
qsub script<\/em><\/pre>\n
script<\/em><\/code> is the name of your jobscript file.<\/p>\nFurther info<\/h2>\n
\n