BLAST Results
Edit and Resubmit [Sign in above to save your search strategy] Formatting options Download How to read this page Blast report description Click here to use the new BLAST results page Questions/comments
Formatting options
Reset form to defaults [?]

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.

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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 dots. more...

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  • Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query. more...
  • NCBI-gi: Show NCBI gi identifiers.
  • CDS feature: Show annotated coding region and translation. more...
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  • Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
  • Masking Color: Display masked sequence regions in the given color.
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  • Descriptions: Show short descriptions for up to the given number of sequences.
  • Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.
  • Line lenghth: Number of letters to show on one line in an alignment.
Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.
Add organism
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Show only sequences from the given organism.

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Show only those sequences that match the given Entrez query. more...

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Show only sequences with expect values in the given range. more...

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Show only sequences with percent identity values in the given range.

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  • Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, in which sequences found in one round of search are used to build a custom score model for the next round. more...
  • Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.
Download
Alignment
Text XML ASN.1 JSON Seq-align Hit Table(text) Hit Table(csv) Multiple-file XML2 Single-file XML2 Multiple-file JSON Single-file JSON SAM
Search Strategies
ASN.1
PSSM to restart search
PSSM
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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 https://www.ncbi.nlm.nih.gov/books/NBK153387/

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 https://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd
3). "ASN.1". Alignment written out in Abstract Syntax Notation 1.
4). "JSON Seq-align". Alignment written out in JSON.
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.
6). "XML2". New XML format described at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf.
7). "JSON". New JSON format described at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf.
8). "SAM". Sequence Alignment Map format.

XML2 and JSON can be downloaded either as one file per query (multiple-file) or one file for all queries (single-file). These formats are listed as Multiple-file XML2 (and JSON) or Single-file XML (and JSON).

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 https://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra

  • There was a problem with the search. Please, contact Help Desk and include RID HX11AFVP01R

    Problem with taxonomic lookup and/or entrez, please consider changing.

Job title: Nucleotide Sequence

Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for.

RID
HX11AFVP01R (Expires on 07-28 15:37 pm)
Query ID
lcl|Query_20201
Description
None
Molecule type
nucleic acid
Query Length
12
Database Name
Description
Program
BLASTN 2.10.1+

Blast search databases information
Database
Description
Posted Date
Reference
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

  • No significant similarity found. For reasons why,click here

Search Parameters
Search parameter name
Search parameter value
Programblastn
Word size11
Expect value10
Hitlist size500
Match/Mismatch scores2,-3
Gapcosts5,2
Low Complexity FilterYes
Filter string L;m;
Genetic Code1
Database
Database parameter name
Database parameter value
Posted date
Number of letters0
Number of sequences0
Entrez query
Includes: SRX885418
Karlin-Altschul statistics
Params
Ungapped
Gapped
Lambda
K
H
Results Statistics
Results Statistics parameter name
Results Statistics parameter value