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NCBI BLAST+ rpstblastn (version 2.14.1+galaxy2)

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 domain database using a nucleotide query, using the NCBI BLAST+ rpstblastn command line tool.

The protein domain databases use position-specific scoring matrices (PSSMs) and are available for a number of domain collections including:

CDD - NCBI curarated meta-collection of domains, see https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains

Kog - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/

Cog - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/

Pfam - PSSMs from Pfam-A seed alignment database, see http://xfam.org/

Smart - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/

Tigr - PSSMs from TIGRFAM database of protein families, see ftp://ftp.jcvi.org/data/TIGRFAMs/

Prk - PSSms from automatically aligned stable clusters in the Protein Clusters database, see https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters

The exact list of domain databases offered will depend on how your local Galaxy has been configured.


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