NCBI BLAST+ (Nucleotide Databases)


BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your sequence.

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How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Database



Database Name Description Abbreviation
ENA Sequence (formerly EMBL-Bank) ENA Sequence (formerly EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
ENA Sequence Release The quarterly release of the ENA Sequence em_rel
ENA Sequence Environmental Sequences from Environmental Samples. em_rel_env
ENA Sequence EST Environmental em_rel_est_env
ENA Sequence GSS Environmental em_rel_gss_env
ENA Sequence HTC Environmental em_rel_htc_env
ENA Sequence HTG Environmental em_rel_htg_env
ENA Sequence Patent Environmental em_rel_pat_env
ENA Sequence Standard Environmental em_rel_std_env
ENA Sequence STS Environmental em_rel_sts_env
ENA Sequence TSA Environmental em_rel_tsa_env
ENA Sequence Fungi Sequences from Fungi. em_rel_fun
ENA Sequence EST Fungi em_rel_est_fun
ENA Sequence GSS Fungi em_rel_gss_fun
ENA Sequence HTC Fungi em_rel_htc_fun
ENA Sequence HTG Fungi em_rel_htg_fun
ENA Sequence Patent Fungi em_rel_pat_fun
ENA Sequence Standard Fungi em_rel_std_fun
ENA Sequence STS Fungi em_rel_sts_fun
ENA Sequence TSA Fungi em_rel_tsa_fun
ENA Sequence Human Sequences from Human. em_rel_hum
ENA Sequence EST Human em_rel_est_hum
ENA Sequence GSS Human em_rel_gss_hum
ENA Sequence HTC Human em_rel_htc_hum
ENA Sequence HTG Human em_rel_htg_hum
ENA Sequence Patent Human em_rel_pat_hum
ENA Sequence Standard Human em_rel_std_hum
ENA Sequence STS Human em_rel_sts_hum
ENA Sequence Invertebrate Sequences from invertebrate organisms. em_rel_inv
ENA Sequence EST Invertebrate em_rel_est_inv
ENA Sequence GSS Invertebrate em_rel_gss_inv
ENA Sequence HTC Invertebrate em_rel_htc_inv
ENA Sequence HTG Invertebrate em_rel_htg_inv
ENA Sequence Patent Invertebrate em_rel_pat_inv
ENA Sequence Standard Invertebrate em_rel_std_inv
ENA Sequence STS Invertebrate em_rel_sts_inv
ENA Sequence TSA Invertebrate em_rel_tsa_inv
ENA Sequence Mammal Sequences from mammals, excluding rodents and humans. em_rel_mam
ENA Sequence EST Mammal em_rel_est_mam
ENA Sequence GSS Mammal em_rel_gss_mam
ENA Sequence HTC Mammal em_rel_htc_mam
ENA Sequence HTG Mammal em_rel_htg_mam
ENA Sequence Patent Mammal em_rel_pat_mam
ENA Sequence Standard Mammal em_rel_std_mam
ENA Sequence STS Mammal em_rel_sts_mam
ENA Sequence TSA Mammal em_rel_tsa_mam
ENA Sequence Mouse Sequences from mus musculus. em_rel_mus
ENA Sequence EST Mouse em_rel_est_mus
ENA Sequence GSS Mouse em_rel_gss_mus
ENA Sequence HTC Mouse em_rel_htc_mus
ENA Sequence HTG Mouse em_rel_htg_mus
ENA Sequence Patent Mouse em_rel_pat_mus
ENA Sequence Standard Mouse em_rel_std_mus
ENA Sequence STS Mouse em_rel_sts_mus
ENA Sequence Phage Sequences from bacteria phages. em_rel_phg
ENA Sequence GSS Phage em_rel_gss_phg
ENA Sequence HTG Phage em_rel_htg_phg
ENA Sequence Patent Phage em_rel_pat_phg
ENA Sequence Standard Phage em_rel_std_phg
ENA Sequence Plant Sequences from plants. em_rel_pln
ENA Sequence EST Plant em_rel_est_pln
ENA Sequence GSS Plant em_rel_gss_pln
ENA Sequence HTC Plant em_rel_htc_pln
ENA Sequence HTG Plant em_rel_htg_pln
ENA Sequence Patent Plant em_rel_pat_pln
ENA Sequence Standard Plant em_rel_std_pln
ENA Sequence STS Plant em_rel_sts_pln
ENA Sequence TSA Plant em_rel_tsa_pln
ENA Sequence Prokaryote Sequences from prokaryotes. em_rel_pro
ENA Sequence EST Prokaryote em_rel_est_pro
ENA Sequence GSS Prokaryote em_rel_gss_pro
ENA Sequence HTC Prokaryote em_rel_htc_pro
ENA Sequence HTG Prokaryote em_rel_htg_pro
ENA Sequence Patent Prokaryote em_rel_pat_pro
ENA Sequence Standard Prokaryote em_rel_std_pro
ENA Sequence STS Prokaryote em_rel_sts_pro
ENA Sequence TSA Prokaryote em_rel_tsa_pro
ENA Sequence Rodent Sequences from rodents, but not mouse. em_rel_rod
ENA Sequence EST Rodent em_rel_est_rod
ENA Sequence GSS Rodent em_rel_gss_rod
ENA Sequence HTC Rodent em_rel_htc_rod
ENA Sequence HTG Rodent em_rel_htg_rod
ENA Sequence Patent Rodent em_rel_pat_rod
ENA Sequence Standard Rodent em_rel_std_rod
ENA Sequence STS Rodent em_rel_sts_rod
ENA Sequence TSA Rodent em_rel_tsa_rod
ENA Sequence Synthetic Sequences from synthetic constructs. em_rel_syn
ENA Sequence Patent Synthetic em_rel_pat_syn
ENA Sequence Standard Synthetic em_rel_std_syn
ENA Sequence Transgenic Sequences from transgenic contructs. em_rel_tgn
ENA Sequence Standard Transgenic em_rel_std_tgn
ENA Sequence GSS Transgenic em_rel_gss_tgn
ENA Sequence Unclassified Sequences from unspecified origin. em_rel_unc
ENA Sequence EST Unclassified em_rel_est_unc
ENA Sequence Patent Unclassified em_rel_pat_unc
ENA Sequence Standard Unclassified em_rel_std_unc
ENA Sequence Viral Sequences from Viruses. em_rel_vrl
ENA Sequence EST Viral em_rel_est_vrl
ENA Sequence GSS Viral em_rel_gss_vrl
ENA Sequence HTG Viral em_rel_htg_vrl
ENA Sequence Patent Viral em_rel_pat_vrl
ENA Sequence Standard Viral em_rel_std_vrl
ENA Sequence TSA Viral em_rel_tsa_vrl
ENA Sequence Vertebrate Sequences from vertebrates, excluding human, mouse and rodents. em_rel_vrt
ENA Sequence EST Vertebrate em_rel_est_vrt
ENA Sequence GSS Vertebrate em_rel_gss_vrt
ENA Sequence HTC Vertebrate em_rel_htc_vrt
ENA Sequence HTG Vertebrate em_rel_htg_vrt
ENA Sequence Patent Vertebrate em_rel_pat_vrt
ENA Sequence Standard Vertebrate em_rel_std_vrt
ENA Sequence STS Vertebrate em_rel_sts_vrt
ENA Sequence TSA Vertebrate em_rel_tsa_vrt
ENA Sequence Updates Daily updates to the quarterly ENA Sequence release emnew
ENA Coding Sequence Release The nucleotide sequences of the ENA Coding Sequence Release. em_cds_rel
ENA Coding Sequence Updates The nucleotide sequences of the ENA Coding Sequence Updates. em_cds_cum
ENA Non-Coding Sequence Release The nucleotide sequences of the ENA Coding Sequence Release. em_ncr_rel
ENA Non-Coding Sequence Updates The nucleotide sequences of the ENA Non-Coding Sequence Updates. em_ncr_cum
ENA Geospatial Release The nucleotide sequences of the ENA Geospatial Sequence Release. em_geo_rel
ENA Geospatial Updates The nucleotide sequences of the ENA Geospatial Sequence Updates. em_geo_cum
ENA Sequence Expressed Sequence Tag em_rel_est
ENA Sequence Genome Survey Sequence em_rel_gss
ENA Sequence High Throughput cDNA em_rel_htc
ENA Sequence High Throughput Genome em_rel_htg
ENA Sequence Patent em_rel_pat
ENA Sequence Standard em_rel_std
ENA Sequence Sequence Tagged Site em_rel_sts
ENA Sequence Transcriptome Shotgun Assembly em_rel_tsa
ENA Sequence Release and Updates emall
ENA Sequence Vectors Sequencing vectors extracted from the ENA Sequence emvec
IMGT/LIGM-DB The immunoglobulins and T cell receptors (LIGM-DB) section of the international immunogenetics (IMGT) database imgtligm
IMGT/HLA The human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) database imgthla
IPD-KIR Human Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD) ipdkir
IPD-MHC Major Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD) ipdmhc
NR Patent DNAs Level-1 Non-redundant Patent DNAs sequences Level 1 covering patent data from the ENA Sequence nrnl1
NR Patent DNAs Level-2 Non-redundant Patent DNAs sequences Level 2 covering patent data from the ENA Sequence nrnl2
Nucleotide Structure Sequences Nucleotide sequences from structures described in the Brookhaven Protein Data Bank(PDB) pdbna

Default value is: ENA Sequence TSA Vertebrate [em_rel_tsa_vrt]

Step 2 - Sequence

Sequence Input Window

The query sequence can be entered directly into this form. The sequence can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing a valid sequence in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processors files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.

Sequence Type

Indicates if the sequence is protein or DNA/RNA.

Type Abbreviation
PROTEIN protein

Default value is: DNA/RNA [dna]

Step 3 - Parameters


The BLAST program to be used for the Sequence Similarity Search.

Program Name Description Abbreviation
blastn Compares a nucleotide sequence (DNA/RNA) to a nucleotide sequence database blastn
tblastx Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that TBLASTX is extremely slow and cpu-intensive. tblastx
tblastn Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames. tblastn

Default value is: blastn


Task option (only selectable for blastn)

Task Name Description Abbreviation
blastn Traditional BLASTN task blastn
megablast Megablast task for quickly searching very similar (e.g., intraspecies or closely related species) sequences megablast

Default value is: blastn


(Protein searches) The substitution matrix used for scoring alignments when searching the database.

Matrix Name Abbreviation
PAM250 PAM250

Default value is: BLOSUM62

Additional information


(Nucleotide searches) The match score is the bonus to the alignment score when matching the same base. The mismatch is the penalty when failing to match.

Match/mismatch_scores Name Abbreviation
1,-4 1,-4
2,-7 2,-7
1,-3 1,-3
2,-5 2,-5
1,-2 1,-2
2,-3 2,-3
1,-1 1,-1
5,-4 5,-4
4,-5 4,-5

Default value is: 1,-3

Gap Open Penalty

Penalty taken away from the score when a gap is created in sequence. Increasing the gap openning penalty will decrease the number of gaps in the final alignment.

Default value is: default [-1]

Additional information

Gap Extend Penalty

Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment.

Default value is: default [-1]

Additional information

Gap Align

This is a true/false setting that tells the program the perform optimised alignments within regions involving gaps. If set to true, the program will perform an alignment using gaps. Otherwise, if it is set to false, it will report only individual HSP where two sequence match each other, and thus will not produce alignments with gaps.

Default value is: true

Additional information

Expectation Threshold

Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.

Default value is: 10 (default) [10]


Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.

Default value is: yes [T]


The amount a score can drop before gapped extension of word hits is halted

Default value is: 0 (default) [0]


Maximum number of match score summaries reported in the result output.

Default value is: 50 (default) [50]


Maximum number of match alignments reported in the result output.

Default value is: 50 (default) [50]

Sequence Range

Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell BLAST to only use residues 34 to 89, inclusive.

Default value is: START-END

Alignment Views

Formating for the alignments

Name Description Value
pairwise The query and match are output as a pairwsie alignment with a consensus line between the two sequences. In the consensus the match states are represented as: identical match as the base/residue, similarity as a '+' and missmatch as a space. 0
Query-anchored identities The matches found are shown relative to the ungapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line. 1
Query-anchored non-identities The matches found are shown relative to the ungapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line. 2
Flat query-anchored identities The matches found are shown relative to the gapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-). 3
Flat query-anchored non-identities The matches found are shown relative to the gapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-). 4
BLASTXML Output NCBI BLAST XML instead of a plain text report. 5
tabular Summary output in tabular format. 6
tabular with comment lines Summary output in tabular format. 7
Text ASN.1 Output in ASN.1 format. 8
Binary ASN.1 Output in ASN.1 format. 9
Comma-separated values Summary output as comma separated values. 10
BLAST archive format (ASN.1) Output in BLAST archive format (ASN.1). 11

Default value is: pairwise [0]

Composition-based Statistics

Use composition-based statistics.

Name Description Value
F (default) No composition-based statistics F
D (equivalent to 2) D
1 Composition-based statistics as in NAR 29:2994-3005, 2001 1
2 Composition-based score adjustment as in Bioinformatics 21:902-911,2005, conditioned on sequence properties 2
3 Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally 3

Default value is: F (default) [F]

Translation Table

Query Genetic code to use in translation

Name Value
N/A -1
Standard SGC0 1
Vertebrate Mitochondrial 2
Yeast Mitochondrial 3
Mold Mitochondrial Protozoan Mitochondrial Coelenterate 4
Invertebrate Mitochondrial 5
Ciliate Nuclear Dasycladacean Nuclear Hexamita Nuclear 6
Echinoderm Mitochondrial Flatworm Mitochondrial 9
Euplotid Nuclear 10
Bacterial and Plant Plastid 11
Alternative Yeast Nuclear 12
Ascidian Mitochondrial 13
Alternative Flatworm Mitochondrial 14
Blepharisma Macronuclear 15
Chlorophycean Mitochondrial 16
Trematode Mitochondrial 21
Scenedesmus obliquus Mitochondrial 22
Thraustochytrium Mitochondrial 23

Default value is: Standard SGC0 [1]

Step 4 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).


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