Note. Database searches may take a substantial amount of time. For large input datasets it is advisable to allow overnight processing.
What it does
Search a protein database using a translated nucleotide query, using the NCBI BLAST+ blastx command line tool.
You can also search against a FASTA file of subject (target) sequences. This is not advised because it is slower (only one CPU is used), but more importantly gives e-values for pairwise searches (very small e-values which will look overly signficiant). In most cases you should instead turn the other FASTA file into a database first using makeblastdb and search against that.
Output format
Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. The standard BLAST+ tabular output contains 12 columns:
| Column | NCBI name | Description |
| 1 | qaccver | Query accession dot version |
| 2 | saccver | Subject accession dot version (database hit) |
| 3 | pident | Percentage of identical matches |
| 4 | length | Alignment length |
| 5 | mismatch | Number of mismatches |
| 6 | gapopen | Number of gap openings |
| 7 | qstart | Start of alignment in query |
| 8 | qend | End of alignment in query |
| 9 | sstart | Start of alignment in subject (database hit) |
| 10 | send | End of alignment in subject (database hit) |
| 11 | evalue | Expectation value (E-value) |
| 12 | bitscore | Bit score |
Until BLAST+ 2.5.0, the first two columns were qseqid and sseqid, which were usually strings contained multiple pipe-separated entries. In BLAST+ 2.5.0, the first two columns became qacc and sacc (accesion only), while in BLAST+ 2.6.0 this was changed again to use qaccver and saccver (accession dot version).
The BLAST+ tools can optionally output additional columns of information, but this takes longer to calculate. Many commonly used extra columns are included by selecting the extended tabular output. The extra columns are included after the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 25 column tabular BLAST output. Galaxy now uses this extended 25 column output by default.
| Column | NCBI name | Description |
| 13 | sallseqid | All subject Seq-id(s), separated by a ';' |
| 14 | score | Raw score |
| 15 | nident | Number of identical matches |
| 16 | positive | Number of positive-scoring matches |
| 17 | gaps | Total number of gaps |
| 18 | ppos | Percentage of positive-scoring matches |
| 19 | qframe | Query frame |
| 20 | sframe | Subject frame |
| 21 | qseq | Aligned part of query sequence |
| 22 | sseq | Aligned part of subject sequence |
| 23 | qlen | Query sequence length |
| 24 | slen | Subject sequence length |
| 25 | salltitles | All subject title(s), separated by a '<>' |
The third option is to customise the tabular output by selecting which columns you want, from the standard set of 12, the default set of 25, or any of the additional columns BLAST+ offers (including species name).
The fourth option is BLAST XML output, which is designed to be parsed by another program, and is understood by some Galaxy tools.
You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. The two query anchored outputs show a multiple sequence alignment between the query and all the matches, and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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