These options control formatting of alignments in results pages. The
default is HTML, but other formats (including plain text) are available.
PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
The Advanced view option allows the database descriptions to be sorted by various indices in a table.
Choose how to view alignments.
The default "pairwise" view shows how each subject sequence aligns
individually to the query sequence. The "query-anchored" view shows how
all subject sequences align to the query sequence. For each view type,
you can choose to show "identities" (matching residues) as letters or
Show only sequences from the given organism.
Show only those sequences that match the given Entrez query.
Show only sequences with expect values in the given range.
Show only sequences with percent identity values in the given range.
The Download link provides BLAST output that may be used as input to another program.
This includes parseable formats such as the tabular report or XML as well as the Search Strategy files read by the BLAST+ applications.
More details on the parseable (XML, tabular, and ASN.1) reports can be found at
The following formats are offered under the Alignment section:
1). "Text". Non-HTML standard BLAST report.
2). "XML". XML report based upon the DTD at http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd
3). "ASN.1" Alignment. This is the alignment written out in Abstract Syntax Notation 1.
4). "Hit Table(text)". The tabular report as text.
5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.
The following report is offered under the Search Strategy section:
1). "ASN.1" Search Strategy. A record of the parameters, query, and database used in the search. This file can be used to start a stand-alone BLAST search, see
Your BLAST job specified more than one input sequence.
This box lets you choose which input sequence to show BLAST results for.
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five
different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected
by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top,
clicking on a hit sequence takes the user to the associated alignments.
This graphic is an overview of database sequences aligned to the query sequence.
Alignments are color-coded by score, within one of five score ranges.
Multiple alignments on the same database sequence are connected by a dashed line.
Mousing over an alignment shows the alignment definition and score in the box at the top.
Clicking an alignment displays the alignment detail.