SWeBLAST Divides a query sequence, or sequences
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SWeBLAST Tags

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SWeBLAST Description

SWeBLAST (Sliding Window WeB-based BLAST) is a command line program written in Perl for use on Windows, Linux and Mac. The main component of SWeBLAST.pl, will divide a query sequence, or sequences, supplied in a FASTA format, into a series of subsequences of chosen length and overlap, and sends these successively to GenBank’s BLAST facility. The search results are collated into a single file, BLAST.TXT, in a sub-folder. This is analyzed by the second component, SWeBLAST_parser.pl, and the results put into a sub-folder as a series of CSV files to be examined using a standard spreadsheet program, such as EXCEL. To look at the available arguments or options, one can run the program using the option -help perl SWeBLAST.pl -help -help or -h : Show this message. -input or -i : Input (data) file. -output or -o : Output folder (OPTIONAL). -window or -w : Window length default 100 (OPTIONAL). -step or -s : Step length - default 50 (OPTIONAL). -database or -d : Genbank Database to be searched - default nr (OPTIONAL). -program or -p : Program to be used : blastn, blastp, blastx - default blastn (OPTIONAL). -expect or -e : EXPECT (OPTIONAL). -entrez or -q : ENTREZ QUERY (OPTIONAL) Boolean command to limit BLAST search (e.g. “virus NOT potato virus Y ”). -parse or -r : to call SWeBLAST_parser.pl (OPTIONAL). -cutoff or -c : discards hits with a greater e-value (OPTIONAL). or use the interactive menu by running the program without arguments and follow the prompt: perl SWeBLAST.pl

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