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).
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
The databases to run the sequence similarity search against. Multiple databases can be used at the same time
|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 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 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.
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.
Default value is: DNA [dna]
Step 3 - Parameters
The FASTA program to be used for the Sequence Similarity Search
|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]
(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|
Default value is: N/A [none]
Additional information Read more about matrices
(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.
Default value is: +5/-4
Gap Open Penalty
Score for the first residue in a gap.
Default value is: -14
Additional information Read more about gap penalties
Gap Extend Penalty
Score for each additional residue in a gap.
Default value is: -4
Additional information Read more about gap penalties
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.
Default value 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) 
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.
Default value is: both
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 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.
|none||No filtering of the query sequence.|
|dust||Uses the DUST filter (Tatusov and Lipman) to mask simple repeats in DNA/RNA sequences.|
Default value is: none
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.
|Regress||Uses a weighted regression of average score vs library sequence length.||1|
|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|
Default value is: Regress 
Maximum number of match score summaries reported in the result output.
Default value is: 50
Maximum number of match alignments reported in the result output.
Default value is: 50
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
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
Turn on/off the display of all significant alignments between query and library sequence.
Default value is: no [false]
Different score report formats.
|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]
Query Genetic code to use in translation
|Mold Mitochondrial Protozoan Mitochondrial Coelenterate||4|
|Ciliate Nuclear Dasycladacean Nuclear Hexamita Nuclear||6|
|Echinoderm Mitochondrial Flatworm Mitochondrial||9|
|Bacterial and Plant Plastid||11|
|Alternative Yeast Nuclear||12|
|Alternative Flatworm Mitochondrial||14|
|Scenedesmus obliquus Mitochondrial||22|
Default value is: Standard 
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.
Step 4 - Submission
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.
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.
If email notification is requested, then a valid Internet email address in the form firstname.lastname@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).
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
(1991 November 01) Genomics 11 (3) :635-650
PMID: 1774068 Rapid and sensitive sequence comparison with FASTP and FASTA.
(1990 January 01) Methods in enzymology 183 :63-98
PMID: 2156132 Improved tools for biological sequence comparison.
(1988 April 01) Proceedings of the National Academy of Sciences of the United States of America 85 (8) :2444-2448
PMID: 3162770 The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596 Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600
Support: For Support on this service: Please contact EMBL-EBI support at http://www.ebi.ac.uk/support/FASTA The Author: William R. Pearson (email: email@example.com) Department of Biochemistry Box 440, Jordan Hall U. of Virginia Charlottesville, VA