What it does

Extracts FASTA formatted sequences from a BLAST database using the NCBI BLAST+ blastdbcmd command line tool.

When giving a text file of entries, use one line per sequence. Optional valies should be space separate - the simplest syntax is identifier start-end (where end can be just -), or identifier start-end strand (wheere the strand given as either + or -).

BLAST assigned identifiers

When a BLAST database is constructed from a FASTA file, the original identifiers can be replaced with BLAST assigned identifiers, partly to ensure uniqueness. e.g. Sometimes a prefix of 'lcl|' is added (lcl is short for local), or an arbitrary name starting 'gnl|BL_ORD_ID|' is created.

If you are using the tabular output from BLAST, it will contain the original identifiers - not the BLAST assigned identifiers suitable for use with the blastdbcmd tool.

If you are using the XML or plain text output, this will also contain the BLAST assigned identifiers. However, this means getting a list of BLAST assigned identifiers isn't straightforward.

Advanced Options

For help with advanced options and their default values, visit the NCBI BLAST® Command Line Applications User Manual, Appendices, Options for the command-line applications.

For amino acid substitution matrices, see BLAST Substitution Matrices in the same appendices.

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). NCBI BLAST+ integrated into Galaxy. GigaScience 4:39 https://doi.org/10.1186/s13742-015-0080-7

Christiam Camacho et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 15;10:421. https://doi.org/10.1186/1471-2105-10-421

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus