BLAST Search

BLAST Search webserver overview

BLAST Search runs NCBI BLAST+ 2.17.0+ protein searches against fixed Swiss-Prot or PDB protein database snapshots on ProteinIQ infrastructure. It supports blastp, blastp-fast, and blastp-short, returning hit tables, alignments, native reports, and database provenance. Queries are not sent to NCBI's public search service.

BLAST Search is currently unavailable while release verification is completed.

Pricing

Searches start at 10 credits. The exact quote is calculated before submission from the total query residues across all records in a job. FASTA headers, whitespace, and gap characters (- and .) do not count toward the quote. Optional filter and strategy files do not add query residues.

These examples use protein FASTA input and the current calculator. Database choice, task, search controls, and report format do not change the quote. Batch runs are quoted as separate jobs for their expanded query inputs.

Inputs

Each input accepts pasted text or one file, with a 50 MiB file limit. Staged inputs also have a combined 50 MiB submission limit. Query and optional file bytes are preserved; BLAST handles sequence parsing, ambiguous amino acids, and matrix/gap feasibility. Identifier lists use the native BLAST file syntax, normally one identifier per line.

Only one GI, sequence ID, or taxonomy include/exclude filter may be supplied, counting both files and taxonomy settings. IPG lists are separate controls. Taxonomy descendant expansion cannot be disabled when a GI or sequence ID list is supplied.

When a strategy is imported, BLAST reads its search settings from that file. The separately submitted query and selected hosted database take precedence. Import and export are mutually exclusive, so strategy.asn1 retains the imported strategy unchanged instead of exporting a replacement. See NCBI's strategy documentation.

Batch mode expands up to 10 query inputs into separate jobs. Multiple records within one query input remain together in that job; optional lists and settings are shared across the batch. Workflows can consume the native files and HSP rows.

Databases and attribution

These are NCBI-distributed snapshots, rather than live database searches. Prepared sequence and taxonomy files are used without scientific modification. Snapshot dates, archive checksums, individual file checksums, and database identity accompany successful results.

BLAST is public-domain software. UniProt and NCBI cannot grant unrestricted permission for third-party patents or other rights covering individual data. The exact BLAST license and database attribution accompany the downloads.

Settings

Empty optional fields leave the corresponding option unset, preserving BLAST's task-dependent defaults. Numeric controls shown as text fields accept numeric text. Native BLAST checks additional task, matrix, and gap-cost constraints.

Search selection

With scoring fields empty, blastp-short uses word size 2, matrix PAM30, gap opening cost 9, and gap extension cost 1. These values are task defaults, not values automatically entered into the form.

Advanced search settings

Culling and Best-Hit controls are mutually exclusive, as are soft and hard database masks. max_target_seqs cannot be combined with num_descriptions or num_alignments. Database masking requires an algorithm present in the selected snapshot; an unavailable algorithm produces a native BLAST error. NCBI describes the Best-Hit filtering criteria in detail.

Native report format

With output_fields empty, tabular formats use BLAST's standard columns. This setting changes the selected report, while hits.tsv retains its fixed 35-column schema. BLAST determines which report options apply to each format.

Outputs

The Hits tab contains one row per native high-scoring segment pair (HSP), in BLAST's original order. Alignments presents the pairwise report, and Files provides native downloads.

A valid search with no matches retains its empty hit table and native reports. Failed searches retain available partial files and logs.

Native reports are generated with separate blastp invocations using the same query, database, and search settings. This preserves statistics that archive replay can omit. Report formatting controls apply to the selected report, except that num_alignments is also supplied to the fixed report searches. ProteinIQ does not calculate replacement scientific scores.

Understanding results

A sequence match alone does not establish biological function. Coverage, alignment extent, database context, and annotation should be considered alongside scores.

The NCBI BLAST+ manual defines native options and reports. The method is described by Altschul et al. (1997).