Formatting options Download How to read this page Blast report description Questions/comments

Formatting options
Show	Alignment as Reset form to defaults Help 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.
Alignment View	Help 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...
Display	Graphical Overview Linkout Sequence Retrieval NCBI-gi CDS feature Help 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...
Masking	Character: Color: Help 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.
Limit results	Descriptions: Graphical overview: Alignments: Line length: Help 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.
	Organism Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown. exclude Help Show only sequences from the given organism.
	Entrez query: Help Show only those sequences that match the given Entrez query. more...
	Expect Min: Expect Max: Help Show only sequences with expect values in the given range. more...
	Percent Identity Min: Percent Identity Max: Help Show only sequences with percent identity values in the given range.
Format for	PSI-BLAST with inclusion threshold: Help 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	[?]

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

Vecscreen

Job title: gnl|VecScreen|Example Database sequence

Interpretation of VecScreen Results

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

RID: JGVZM27F015 (Expires on 11-05 13:55 pm)

Query ID: lcl|Query_125685; lcl|Query_125685
Description: gnl|VecScreen|Example Database sequence with vector contamination
Molecule type: nucleic acid
Query Length: 1057


Database Name: screen/UniVec
Description: UniVec (build 10.0) See details
Program: BLASTN 2.16.1+ Citation

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.

Other reports: Search Summary [Distance tree of results]

Search Parameters
Search parameter name	Search parameter value
Program	blastn
Word size	11
Expect value	700
Hitlist size	1000
Match/Mismatch scores	1,-5
Gapcosts	3,3
Low Complexity Filter	Yes
Filter string	L;m;
Genetic Code	1

Database
Database parameter name	Database parameter value
Posted date	Mar 20, 2017 3:58 PM
Number of letters	1,269,791
Number of sequences	6,093
Entrez query	Includes: Excludes: None

Karlin-Altschul statistics
Params	Ungapped	Gapped
Lambda	1.38556	1.39
K	0.746509	0.747
H	1.37945	1.38

Results Statistics
Results Statistics parameter name	Results Statistics parameter value
Length adjustment	14
Effective length of query	1043
Effective length of database	1184489
Effective search space	1235422027
Effective search space used	1750000000000

Descriptions

Sequences producing significant alignments:

Select:All None Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reports	Description	Max Score	Total Score	Query Cover	E value	Per. Ident
1Select seq gnl\|BL_ORD_ID\|5887	gnl\|uv\|KM407505.1:939-2365 Cloning vector pCK903	84.6	84.6	4%	6e-14	98.00%
2Select seq gnl\|BL_ORD_ID\|3830	gnl\|uv\|U02448.1:3446-3536 Cloning vector pMAMneo-LUC	44.5	44.5	2%	0.068	100.00%
3Select seq gnl\|BL_ORD_ID\|3309	gnl\|uv\|U13860.1:6124-7626-49 pMSG cloning vector	32.5	32.5	1%	287	100.00%

Job title: gnl|VecScreen|Example Database sequence

Graphic Summary

Distribution of the top 3 Blast Hits on 3 subject sequences [?]

Descriptions

Alignments