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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

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...) (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

Database NameDescriptionAbbreviation
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 ReleaseThe quarterly release of the ENA Sequenceem_rel
ENA Sequence EnvironmentalSequences 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 FungiSequences 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 HumanSequences 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 InvertebrateSequences 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 MammalSequences 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 MouseSequences 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 PhageSequences 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 PlantSequences 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 ProkaryoteSequences 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 RodentSequences 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 SyntheticSequences from synthetic constructs.em_rel_syn
ENA Sequence Patent Synthetic
em_rel_pat_syn
ENA Sequence Standard Synthetic
em_rel_std_syn
ENA Sequence TransgenicSequences from transgenic contructs.em_rel_tgn
ENA Sequence Standard Transgenic
em_rel_std_tgn
ENA Sequence GSS Transgenic
em_rel_gss_tgn
ENA Sequence UnclassifiedSequences 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 ViralSequences 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 VertebrateSequences 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 UpdatesDaily updates to the quarterly ENA Sequence releaseemnew
ENA Coding Sequence ReleaseThe nucleotide sequences of the ENA Coding Sequence Release.em_cds_rel
ENA Coding Sequence UpdatesThe nucleotide sequences of the ENA Coding Sequence Updates.em_cds_cum
ENA Non-Coding Sequence ReleaseThe nucleotide sequences of the ENA Coding Sequence Release.em_ncr_rel
ENA Non-Coding Sequence UpdatesThe nucleotide sequences of the ENA Non-Coding Sequence Updates.em_ncr_cum
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
ENA Sequence Release and Updates
emall
ENA Sequence VectorsSequencing vectors extracted from the ENA Sequenceemvec
IMGT

IMGT/LIGM-DBThe immunoglobulins and T cell receptors (LIGM-DB) section of the international immunogenetics (IMGT) databaseimgtligm
IMGT/HLAThe human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) databaseimgthla
IPD-KIRHuman Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD)ipdkir
IPD-MHCMajor Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD)ipdmhc
Patents

NR Patent DNAs Level-1Non-redundant Patent DNAs sequences Level 1 covering patent data from the ENA Sequencenrnl1
NR Patent DNAs Level-2Non-redundant Patent DNAs sequences Level 2 covering patent data from the ENA Sequencenrnl2
Structure

Nucleotide Structure SequencesNucleotide 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.

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.

TypeAbbreviation
PROTEINprotein
DNAdna
RNArna

Default value is: DNA [dna]

Step 3 - Parameters

Program

The FASTA program to be used for the Sequence Similarity Search

Program NameDescriptionAbbreviation
FASTAScan a protein or DNA sequence library for similar sequences.fasta
SSEARCHCompare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm.ssearch
GGSEARCHCompare a protein or DNA sequence to a sequence database using a global alignment (Needleman-Wunsch)ggsearch
GLSEARCHCompare 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
TFASTXCompare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations.tfastx
TFASTYCompare 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 NameTarget IdentityAbbreviation
BLOSUM5025%BL50
BLASTP6230%BP62
BLOSUM8040%BL80
PAM25020%P250
PAM12035%P120
MDM4065%M40
MDM2085%M20
MDM1090%M10
VTML16025%VT160
VTML12035%VT120
VTML8040%VT80
VTML4065%VT40
VTML2085%VT20
VTML1090%VT10
N/ANonenone

Default value 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.

Match/mismatch_scoresAbbreviation
+5/-4+5/-4
+3/-2+3/-2
N/Anone

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

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.

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) [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 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.

ValueDescription
noneNo filtering of the query sequence.
dustUses the DUST filter (Tatusov and Lipman) to mask simple repeats in DNA/RNA sequences.

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.

NameDescriptionValue
RegressUses a weighted regression of average score vs library sequence length.1
MLEUses Maximum Likelihood Estimates of Lambda and K.2
Altshul-GishUses 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 [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.

NameDescriptionValue
DefaultDefault FASTA score formatdefault
-m 8 -- blast tabularTo output BLAST tabular format.8
-m 8C -- BLAST tabular with commentsTo output format.8C
-m 8Cc -- BLAST tabular with -m 9c alignment encoding and domain informationTo output BLAST tabular with -m 9c alignment encoding and domain information format.8Cc
-m 8CC -- BLAST tabular with CIGAR and domain informationTo output BLAST tabular with CIGAR and domain information format.8CC
-m 8CD -- BLAST tabular with variation and domain informationTo output BLAST tabular with variation and domain information.8CD
-m 9 -- with coordinates scores and %identityTo extend scores report with coordinates scores and %identity.9
-m 9C -- with CIGAR alignmentTo display an alignment code in CIGAR format.9C
-m 9c -- with encoded alignmentTo extend scores report with coordinate, %identity and encoded alignment details.9c
-m 9i -- with identity and lengthTo extend scores report with %identity and length only.9i

Default value is: Default [default]

Translation Table

Query Genetic code to use in translation

NameValue
N/A-1
Standard1
Vertebrate Mitochondrial2
Yeast Mitochondrial3
Mold Mitochondrial Protozoan Mitochondrial Coelenterate4
Invertebrate Mitochondrial5
Ciliate Nuclear Dasycladacean Nuclear Hexamita Nuclear6
Echinoderm Mitochondrial Flatworm Mitochondrial9
Euplotid Nuclear10
Bacterial and Plant Plastid11
Alternative Yeast Nuclear12
Ascidian Mitochondrial13
Alternative Flatworm Mitochondrial14
Blepharisma Macronuclear15
Chlorophycean Mitochondrial16
Trematode Mitochondrial21
Scenedesmus obliquus Mitochondrial22
Thraustochytrium Mitochondrial23

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.

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).

References

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
PMID: 23671338

Contact details

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: wrp@virginia.edu) Department of Biochemistry Box 440, Jordan Hall U. of Virginia Charlottesville, VA 

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