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 protein query, using the NCBI BLAST+ blastp command line tool.
The search can be performed using a local database, against a sequence supplied in a fasta file, or the blast can be performed remotely at NCBI.
The remote operation allows searches to be targeted at specific organisms.
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 | qseqid | Query Seq-id (ID of your sequence) |
| 2 | sseqid | Subject Seq-id (ID of the 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 |
The BLAST+ tools can optionally output additional columns of information, but this takes longer to calculate. Most (but not all) of these 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 24 column tabular BLAST output.
| 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 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).
References
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.