NCBI BLAST+ (Nucleotide Databases)
Introduction
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.
- Official Website
- Download Software
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
Databases
Database
| Database Name | Description | Abbreviation |
|---|---|---|
| ENA Sequence | 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 Coding Sequence Release | The nucleotide sequences of the ENA Coding Sequence Release. | em_cds_rel |
| ENA Non-Coding Sequence Release | The nucleotide sequences of the ENA Coding Sequence Release. | em_ncr_rel |
| Others | ||
| 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 |
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 |
| DNA/RNA | dna |
Default value is: DNA/RNA [dna]
Step 3 - Parameters
Program
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
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
Matrix
(Protein searches) The substitution matrix used for scoring alignments when searching the database.
| Matrix Name | Abbreviation |
|---|---|
| BLOSUM45 | BLOSUM45 |
| BLOSUM50 | BLOSUM50 |
| BLOSUM62 | BLOSUM62 |
| BLOSUM80 | BLOSUM80 |
| BLOSUM90 | BLOSUM90 |
| PAM30 | PAM30 |
| PAM70 | PAM70 |
| PAM250 | PAM250 |
Default value is: BLOSUM62
- Additional information
Match/mismatch_scores
(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
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]
Dropoff
The amount a score can drop before gapped extension of word hits is halted
Default value is: 0 (default) [0]
Scores
Maximum number of match score summaries reported in the result output.
Default value is: 50 (default) [50]
Alignments
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 joe@example.org 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).