Introduction
FASTA (pronounced FAST-AYE) is a suite of programs for searching nucleotide or protein databases with a query sequence. FASTA itself performs a local heuristic search of a protein or nucleotide database for a query of the same type. FASTX and FASTY translate a nucleotide query for searching a protein database. TFASTX and TFASTY translate a nucleotide database to be searched with a protein query. Optimal searches are available with the programs SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query against local database).
Official Website
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Important Note
- We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.
How to Access FASTA
FASTA can be accessed via
Web Form
Web interface for FASTA is available at :
https://www.ebi.ac.uk/Tools/sss/fasta/ (Protein)
https://www.ebi.ac.uk/Tools/sss/fasta/nucleotide.html (Nucleotide)
https://www.ebi.ac.uk/Tools/sss/fasta/genomes.html (Genome)
https://www.ebi.ac.uk/Tools/sss/fasta/wgs.html (Whole Genome)
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...) (See example input formats)
- In the following steps, the user has the possibility to change the default tool parameters (See example output formats)
- 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
The databases to run the sequence similarity search against. Multiple databases can be used at the same time. See Databases to run SSS against FASTA for more details.
Step 2 - Sequence
Sequence Input Window
The query sequence can be entered directly into this form. The sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) 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 (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) 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 query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.
| Type | Abbreviation |
|---|---|
| PROTEIN | protein |
| DNA | dna |
| RNA | rna |
Default value (for Protein FASTA) is: PROTEIN [protein]
Default value (for Nucleotide, Genome and Whole Genome Shotgun FASTA) is: DNA [dna]
Step 3 - Parameters
Program
The FASTA program to be used for the Sequence Similarity Search
For Protein FASTA:
| Program Name | Description | Abbreviation |
|---|---|---|
| FASTA | Scan a protein or DNA sequence library for similar sequences. | fasta |
| FASTX | Compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames. | fastx |
| FASTY | Compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames. | fasty |
| SSEARCH | Compare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm. | ssearch |
| GGSEARCH | Compare a protein or DNA sequence to a sequence database using a global alignment (Needleman-Wunsch) | ggsearch |
| GLSEARCH | Compare a protein or DNA sequence to a sequence database with alignments that are global in the query and local in the database sequence (global-local). | glsearch |
For Nucleotide/Genome/Whole Genome Shotgun
| Program Name | Description | Abbreviation |
|---|---|---|
| FASTA | Scan a protein or DNA sequence library for similar sequences. | fasta |
| SSEARCH | Compare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm. | ssearch |
| GGSEARCH | Compare a protein or DNA sequence to a sequence database using a global alignment (Needleman-Wunsch) | ggsearch |
| GLSEARCH | Compare a protein or DNA sequence to a sequence database with alignments that are global in the query and local in the database sequence (global-local). | glsearch |
| TFASTX | Compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations. | tfastx |
| TFASTY | Compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations. | tfasty |
Default value is: FASTA [fasta]
Matrix
(Protein searches) The substitution matrix used for scoring alignments when searching the database. Target identity is the average alignment identity the matrix would produce in the absence of homology and can be used to compare different matrix types. Alignment boundaries are more accurate when the alignment identity matches the target identity percentage.
| Matrix Name | Target Identity | Abbreviation |
|---|---|---|
| BLOSUM50 | 25% | BL50 |
| BLOSUM62 | BL62 | |
| BLASTP62 | 30% | BP62 |
| BLOSUM80 | 40% | BL80 |
| PAM250 | 20% | P250 |
| PAM120 | 35% | P120 |
| MDM40 | 65% | M40 |
| MDM20 | 85% | M20 |
| MDM10 | 90% | M10 |
| VTML160 | 25% | VT160 |
| VTML120 | 35% | VT120 |
| VTML80 | 40% | VT80 |
| VTML40 | 65% | VT40 |
| VTML20 | 85% | VT20 |
| VTML10 | 90% | VT10 |
| N/A | None | None (Only for Nucleotide/Genome/Whole Genome Shotgun) |
Default value for (Protein FASTA) is: BLOSUM50 [BL50]
Default value for (Nucleotide/Genome/Whole Genome Shotgun) is: N/A [none]
Additional information Read more about matrices
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.
For Protein
| Match/mismatch_scores | Abbreviation |
|---|---|
| N/A | none |
For Nucleotide/Genome/Whole Genome Shotgun
| Match/mismatch_scores | Abbreviation |
|---|---|
| +5/-4 | +5/-4 |
| +3/-2 | +3/-2 |
| N/A | none |
Default value is: +5/-4
Gap Open Penalty
Score for the first residue in a gap.
Values: default, 0 to -25, -30, -32, -35, -40, -50, -64
Default value for (Protein FASTA) is: -10
Default value for (Nucleotide) is: -14
Default value for (Genome/Whole Genome Shotgun) is: -16
Additional information Read more about gap penalties
Gap Extend Penalty
Score for each additional residue in a gap.
Values: default, 0 to -8, -16
Default value for (Protein FASTA) is: -2
Default value for (Nucleotide/Genome/Whole Genome Shotgun) is: -4
Additional information Read more about gap penalties
KTUP
FASTA uses a rapid word-based lookup strategy to speed the initial phase of the similarity search. The KTUP is used to control the sensitivity of the search. Lower values lead to more sensitive, but slower searches.
Values(Protein): 1,2
Values (Nucleotide/Genome/Whole Genome Shotgun): 2 to 6
Default value (for Protein) is: 2
Default value for (Nucleotide/Genome/Whole Genome Shotgun) is: 6
Expectation Upper Limit
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
Expectation Lower Limit
Limit the number of scores and alignments reported based on the expectation value. This is the minimum number of times the match is expected to occur by chance. This allows closely related matches to be excluded from the result in favor of more distant relationships.
Default value is: 0 (default) [0]
Strand
For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.
| Value |
|---|
| none |
| both |
| top |
| bottom |
Default value (for Protein) is: N/A [none]
Default value (Nucleotide/Genome/Whole Genome Shotgun) is: both
Histogram
Turn on/off the histogram in the FASTA result. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
Default value is: no [false]
Filter
Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather then meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
| Service | Value | Description |
|---|---|---|
Protein FASTA | seg | Uses the SEQ filter (Wootton and Federhen, 1993) to replace low-complexity regions with 'X' in protein query sequences. |
| xnu | Uses the XNU filter (Claverie and States, 1993) to mask statistically significant tandem repeats in protein query sequences. | |
| seg+xnu | Uses both SEG and XNU to filter low-complexity regions and statistically significant tandem repeats in protein query sequences. | |
| Nucleotide FASTA | dust | Uses the DUST filter (Tatusov and Lipman) to mask simple repeats in DNA/RNA sequences. |
| Protein/Nucleotide/Genome/Whole Genome FASTA | none | No filtering of the query sequence. |
Default value is: none
Statistical Estimates
The statistical routines assume that the library contains a large sample of unrelated sequences. Options to select what method to use include regression, maximum likelihood estimates, shuffles, or combinations of these.
| Service | Name | Description | Value |
|---|---|---|---|
Protein/Nucleotide | MLE | Uses Maximum Likelihood Estimates of Lambda and K. | 2 |
| Altshul-Gish | Uses Altschul-Gish parameters (Altschul and Gish, 1996). | 3 | |
| Regress/shuf. | Estimate the statistical parameters from shuffled copies of each library sequence using the Regress method above. | 11 | |
| MLE/shuf. | Estimate the statistical parameters from shuffled copies of each library sequence using the Maximum Likelihood Estimates method above. | 12 | |
| Protein/Nucleotide/Genome/Whole Genome | Regress | Uses a weighted regression of average score vs library sequence length. | 1 |
Default value is: Regress [1]
Scores
Maximum number of match score summaries reported in the result output.
Default value is: 50
Alignments
Maximum number of match alignments reported in the result output.
Default value is: 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 FASTA to only use residues 34 to 89, inclusive.
Default value is: START-END
Database Range
Specify the sizes of the sequences in a database to search against. For example: 100-250 will search all sequences in a database with length between 100 and 250 residues, inclusive.
Default value is: START-END
HSPs
Turn on/off the display of all significant alignments between query and library sequence.
Default value is: no [false]
Score Format
Different score report formats.
| Name | Description | Value |
|---|---|---|
| Default | Default FASTA score format | default |
| -m 8 -- blast tabular | To output BLAST tabular format. | 8 |
| -m 8C -- BLAST tabular with comments | To output format. | 8C |
| -m 8Cc -- BLAST tabular with -m 9c alignment encoding and domain information | To output BLAST tabular with -m 9c alignment encoding and domain information format. | 8Cc |
| -m 8CC -- BLAST tabular with CIGAR and domain information | To output BLAST tabular with CIGAR and domain information format. | 8CC |
| -m 8CD -- BLAST tabular with variation and domain information | To output BLAST tabular with variation and domain information. | 8CD |
| -m 9 -- with coordinates scores and %identity | To extend scores report with coordinates scores and %identity. | 9 |
| -m 9C -- with CIGAR alignment | To display an alignment code in CIGAR format. | 9C |
| -m 9c -- with encoded alignment | To extend scores report with coordinate, %identity and encoded alignment details. | 9c |
| -m 9i -- with identity and length | To extend scores report with %identity and length only. | 9i |
Default value is: Default [default]
Translation Table
Query Genetic code to use in translation
| Name | Value |
|---|---|
| N/A | -1 |
| Standard | 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 [1]
Annotation Features
Turn on/off annotation features. Annotation features shows features from UniProtKB, such as variants, active sites, phospho-sites and binding sites that have been found in the aligned region of the database hit. To see the annotation features in the results after this has been enabled, select sequences of interest and click to 'Show' Alignments. This option also enables a new result tab (Domain Diagrams) that highlights domain regions.
Default value is: no [false]
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).
FASTA Help and Documentation#Top
Web Services
Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.
For an introduction on how to run these clients and use them in workflows please see the webinar series.
REST API
The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
| Language | Download | Requirements |
|---|---|---|
| Perl | fasta.pl | LWP and XML::Simple |
Python | xmltramp2 |
For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.
WADL
The WADL for the FASTA (REST) service: http://www.ebi.ac.uk/Tools/services/rest/fasta?wadl
FASTA Help and Documentation#Top
SOAP API
The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
WSDL
The WSDL for the FASTA (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/fasta?wsdl
The Kissinger Research Group, University of Georgia provide a SAWSDL for the FASTA (SOAP) web service, which is annotated using OBIws: http://mango.ctegd.uga.edu/jkissingLab/SWS/Wsannotation/resources/fasta.sawsdl
Open API Interface
https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=fasta
List of Endpoints
FASTA Help and Documentation#Top
Common Workflow Language
CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl
For details, see CWL Workflows page.
FASTA Help and Documentation#Top