NCBI BLAST+ (Protein 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 |
|---|---|---|
| UniProt Knowledgebase | The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve "everything that is known" about a particular sequence | uniprotkb |
| UniProtKB/Swiss-Prot | The manually curated subsection of the UniProt Knowledgebase | uniprotkb_swissprot |
| UniProtKB/Swiss-Prot isoforms | The isoform sequences for the manually curated subsection of the UniProt Knowledgebase | uniprotkb_swissprotsv |
| UniProtKB/TrEMBL | Subsection of the UniProt Knowledgebase derived from ENA Sequence (formerly EMBL-Bank) coding sequence translations with annotation produced by an automated process. | uniprotkb_trembl |
| UniProt Clusters | The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed up searches. | |
| UniProt Clusters 100% | The UniProt Reference Clusters (UniRef) containing sequences which are 100% identical. | uniref100 |
| UniProt Clusters 90% | The UniProt Reference Clusters (UniRef) containing sequences which are 90% identical. | uniref90 |
| UniProt Clusters 50% | The UniProt Reference Clusters (UniRef) containing sequences which are 50% identical. | uniref50 |
Default value is: UniProt Knowledgebase [uniprotkb]
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: PROTEIN [protein]
Step 3 - Parameters
Program
The BLAST program to be used for the Sequence Similarity Search.
| Program Name | Description | Abbreviation |
|---|---|---|
| blastp | Compares an amino acid query sequence against a protein sequence database | blastp |
| blastx | Compares a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames | blastx |
Default value is: blastp
Task
Task option (only selectable for blastn)
| Task Name | Description | Abbreviation |
|---|---|---|
| blastp | Default BLASTP task | blastp |
Default value is: blastp
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 |
|---|---|
| N/A |
Default value is: N/A []
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: no [F]
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 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).