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.
- Download Software
- Official Website
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 |
|---|---|---|
| EMBL-Bank | 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. | |
| EMBL Release | The quarterly release of the EMBL nucleotide sequence databank (EMBL-Bank) | em_rel |
| EMBL Environmental | Sequences from Environmental Samples. | em_rel_env |
| EMBL EST Environmental | em_rel_est_env | |
| EMBL GSS Environmental | em_rel_gss_env | |
| EMBL HTC Environmental | em_rel_htc_env | |
| EMBL HTG Environmental | em_rel_htg_env | |
| EMBL Patent Environmental | em_rel_pat_env | |
| EMBL Standard Environmental | em_rel_std_env | |
| EMBL TSA Environmental | em_rel_tsa_env | |
| EMBL Fungi | Sequences from Fungi. | em_rel_fun |
| EMBL EST Fungi | em_rel_est_fun | |
| EMBL GSS Fungi | em_rel_gss_fun | |
| EMBL HTC Fungi | em_rel_htc_fun | |
| EMBL HTG Fungi | em_rel_htg_fun | |
| EMBL Patent Fungi | em_rel_pat_fun | |
| EMBL Standard Fungi | em_rel_std_fun | |
| EMBL STS Fungi | em_rel_sts_fun | |
| EMBL TSA Fungi | em_rel_tsa_fun | |
| EMBL Human | Sequences from Human. | em_rel_hum |
| EMBL EST Human | em_rel_est_hum | |
| EMBL GSS Human | em_rel_gss_hum | |
| EMBL HTC Human | em_rel_htc_hum | |
| EMBL HTG Human | em_rel_htg_hum | |
| EMBL Patent Human | em_rel_pat_hum | |
| EMBL Standard Human | em_rel_std_hum | |
| EMBL STS Human | em_rel_sts_hum | |
| EMBL Invertebrate | Sequences from invertebrate organisms. | em_rel_inv |
| EMBL EST Invertebrate | em_rel_est_inv | |
| EMBL GSS Invertebrate | em_rel_gss_inv | |
| EMBL HTC Invertebrate | em_rel_htc_inv | |
| EMBL HTG Invertebrate | em_rel_htg_inv | |
| EMBL Patent Invertebrate | em_rel_pat_inv | |
| EMBL Standard Invertebrate | em_rel_std_inv | |
| EMBL STS Invertebrate | em_rel_sts_inv | |
| EMBL TSA Invertebrate | em_rel_tsa_inv | |
| EMBL Mammal | Sequences from mammals, excluding rodents and humans. | em_rel_mam |
| EMBL EST Mammal | em_rel_est_mam | |
| EMBL GSS Mammal | em_rel_gss_mam | |
| EMBL HTC Mammal | em_rel_htc_mam | |
| EMBL HTG Mammal | em_rel_htg_mam | |
| EMBL Patent Mammal | em_rel_pat_mam | |
| EMBL Standard Mammal | em_rel_std_mam | |
| EMBL STS Mammal | em_rel_sts_mam | |
| EMBL TSA Mammal | em_rel_tsa_mam | |
| EMBL Mouse | Sequences from mus musculus. | em_rel_mus |
| EMBL EST Mouse | em_rel_est_mus | |
| EMBL GSS Mouse | em_rel_gss_mus | |
| EMBL HTC Mouse | em_rel_htc_mus | |
| EMBL HTG Mouse | em_rel_htg_mus | |
| EMBL Patent Mouse | em_rel_pat_mus | |
| EMBL Standard Mouse | em_rel_std_mus | |
| EMBL STS Mouse | em_rel_sts_mus | |
| EMBL Phage | Sequences from bacteria phages. | em_rel_phg |
| EMBL GSS Phage | em_rel_gss_phg | |
| EMBL HTG Phage | em_rel_htg_phg | |
| EMBL Patent Phage | em_rel_pat_phg | |
| EMBL Standard Phage | em_rel_std_phg | |
| EMBL Plant | Sequences from plants. | em_rel_pln |
| EMBL EST Plant | em_rel_est_pln | |
| EMBL GSS Plant | em_rel_gss_pln | |
| EMBL HTC Plant | em_rel_htc_pln | |
| EMBL HTG Plant | em_rel_htg_pln | |
| EMBL Patent Plant | em_rel_pat_pln | |
| EMBL Standard Plant | em_rel_std_pln | |
| EMBL STS Plant | em_rel_sts_pln | |
| EMBL TSA Plant | em_rel_tsa_pln | |
| EMBL Prokaryote | Sequences from prokaryotes. | em_rel_pro |
| EMBL EST Prokaryote | em_rel_est_pro | |
| EMBL GSS Prokaryote | em_rel_gss_pro | |
| EMBL HTC Prokaryote | em_rel_htc_pro | |
| EMBL HTG Prokaryote | em_rel_htg_pro | |
| EMBL Patent Prokaryote | em_rel_pat_pro | |
| EMBL Standard Prokaryote | em_rel_std_pro | |
| EMBL STS Prokaryote | em_rel_sts_pro | |
| EMBL TSA Prokaryote | em_rel_tsa_pro | |
| EMBL Rodent | Sequences from rodents, but not mouse. | em_rel_rod |
| EMBL EST Rodent | em_rel_est_rod | |
| EMBL GSS Rodent | em_rel_gss_rod | |
| EMBL HTC Rodent | em_rel_htc_rod | |
| EMBL HTG Rodent | em_rel_htg_rod | |
| EMBL Patent Rodent | em_rel_pat_rod | |
| EMBL Standard Rodent | em_rel_std_rod | |
| EMBL STS Rodent | em_rel_sts_rod | |
| EMBL TSA Rodent | em_rel_tsa_rod | |
| EMBL Synthetic | Sequences from synthetic constructs. | em_rel_syn |
| EMBL Patent Synthetic | em_rel_pat_syn | |
| EMBL Standard Synthetic | em_rel_std_syn | |
| EMBL Transgenic | Sequences from transgenic contructs. | em_rel_tgn |
| EMBL Standard Transgenic | em_rel_std_tgn | |
| EMBL GSS Transgenic | em_rel_gss_tgn | |
| EMBL Unclassified | Sequences from unspecified origin. | em_rel_unc |
| EMBL EST Unclassified | em_rel_est_unc | |
| EMBL Patent Unclassified | em_rel_pat_unc | |
| EMBL Standard Unclassified | em_rel_std_unc | |
| EMBL Viral | Sequences from Viruses. | em_rel_vrl |
| EMBL EST Viral | em_rel_est_vrl | |
| EMBL GSS Viral | em_rel_gss_vrl | |
| EMBL HTG Viral | em_rel_htg_vrl | |
| EMBL Patent Viral | em_rel_pat_vrl | |
| EMBL Standard Viral | em_rel_std_vrl | |
| EMBL TSA Viral | em_rel_tsa_vrl | |
| EMBL Vertebrate | Sequences from vertebrates, excluding human, mouse and rodents. | em_rel_vrt |
| EMBL EST Vertebrate | em_rel_est_vrt | |
| EMBL GSS Vertebrate | em_rel_gss_vrt | |
| EMBL HTC Vertebrate | em_rel_htc_vrt | |
| EMBL HTG Vertebrate | em_rel_htg_vrt | |
| EMBL Patent Vertebrate | em_rel_pat_vrt | |
| EMBL Standard Vertebrate | em_rel_std_vrt | |
| EMBL STS Vertebrate | em_rel_sts_vrt | |
| EMBL TSA Vertebrate | em_rel_tsa_vrt | |
| EMBL Updates | Daily updates to the quarterly EMBL nucleotide sequence databank (EMBL-Bank) release | emnew |
| EMBL Coding Sequence | The nucleotide sequences of the coding sequence (CDS) features in the EMBL nucleotide sequence databank (EMBL-Bank). | emblcds |
| Others | ||
| EMBL Expressed Sequence Tag | em_rel_est | |
| EMBL Genome Survey Sequence | em_rel_gss | |
| EMBL High Throughput cDNA | em_rel_htc | |
| EMBL High Throughput Genome | em_rel_htg | |
| EMBL Patent | em_rel_pat | |
| EMBL Standard | em_rel_std | |
| EMBL Sequence Tagged Site | em_rel_sts | |
| EMBL Transcriptome Shotgun Assembly | em_rel_tsa | |
| EMBL Release and Updates | emall | |
| EMBL Vectors | Sequencing vectors extracted from the EMBL nucleotide sequence databank (EMBL-Bank) | emvec |
| IMGT | ||
| 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 |
| Patents | ||
| NR Patent DNAs Level-1 | Non-redundant Patent DNAs sequences Level 1 covering patent data from the EMBL-Bank | nrnl1 |
| NR Patent DNAs Level-2 | Non-redundant Patent DNAs sequences Level 2 covering patent data from the EMBL-Bank | nrnl2 |
| Structure | ||
| Nucleotide Structure Sequences | Nucleotide sequences from structures described in the Brookhaven Protein Data Bank(PDB) | pdbna |
Default value is: EMBL 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
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 |
|---|---|
| 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
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]
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 |
Default value is: pairwise [0]
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).