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johnmay edited this page Jan 7, 2013 · 6 revisions
# Tools

ncbi-blast+

blast-preferences

  • Location of blastp - this is the full path to the ncbi-blast+ blastp on your file system. If you do not have blastp this version is available from the NCBI FTP site (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/). With the blast+ suite installed the path to the blastp program, which is in the bin/ directory of the ncbi-blast+ suite, can be specified. Either enter the path manually or use the browse button to open a file chooser and select the correct file. Example of a complete path: /usr/local/ncbi/blast/bin/blastp.

  • Version of blastp - this is the version of blastp which is being used. This can easily be obtained by invoking >blastp -version on the command line. At the time of writing the current and highest supported version is 2.2.27+. This can be entered as either 2.2.27+ or 2.2.27.

  • Blast Database Root - this is the full path to locally stored blast databases. Database can be downloaded or created using the ncbi-blast+ makeblastdb command. For maximum compatibility the sequence headers should follow the fasta header format. Currently supported identifiers include: SwissProt (sp), TrEMBL (tr) and NCBI Reference Sequence (ref).

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