FASTM (Nucleotide Databases)

Introduction

FASTM --- compare peptides to a protein sequence database.

FAQs
Official Website
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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

The databases to run the sequence similarity search against. Multiple databases can be used at the same time

Database Name Description Abbreviation
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 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 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
EMBL Coding Sequence The nucleotide sequences of the coding sequence (CDS) features in the EMBL nucleotide sequence databank (EMBL-Bank). emblcds
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 Vectors Sequencing vectors extracted from the ENA Sequence 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 ENA Sequence nrnl1
NR Patent DNAs Level-2 Non-redundant Patent DNAs sequences Level 2 covering patent data from the ENA Sequence nrnl2
Structure
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 input set of peptide or nucelotide sequence fragments are described using a modified fasta sequence format. This comprises a fasta header line with an identifier for the set of sequences and optionally a description, followed by the individual sequences each starting on a newline and separated with commas. Partially formatted sequences are 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

The input file containing the set of peptide or nucelotide sequence fragments to search with uses a modified fasta sequence format. This comprises a fasta header line with an identifier for the set of sequences and optionally a description, followed by the individual sequences each starting on a newline and separated with commas. 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
DNA dna
RNA rna

Default value is: DNA [dna]

Step 3 - Parameters

Program

The FASTA program to be used for the Sequence Similarity Search

Program Name Description Abbreviation
FASTM Compare short peptides to a protein sequence database. fastm

Default value is: FASTM [fastm]

Matrix

The comparison matrix to be used to score alignments when searching the database

Matrix Name Abbreviation
N/A none
Additional information

Match/mismatch__scores

Specify match/mismatch scores for DNA comparisons. The default is "+5/-4". "+3/-2" can perform better in some cases.

Match/mismatch_scores Abbreviation
+2/-2 +2/-2
+5/-4 +5/-4
+3/-2 +3/-2
N/A none

Default value is: +2/-2

Gap Open Penalty

Score for the first residue in a gap.

Default value is: -14

Additional information

Gap Extend Penalty

Score for each additional residue in a gap.

Default value is: -4

Additional information

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: 2

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.

Value Description
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

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.

Name Description Value
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 [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 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]

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

Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.
(2002 Feb) Molecular & cellular proteomics : MCP 1 (2) :139-47
Rapid and sensitive sequence comparison with FASTP and FASTA.
(1990) Methods in enzymology 183 :63-98
Improved tools for biological sequence comparison.
(1988 Apr) Proceedings of the National Academy of Sciences of the United States of America 85 (8) :2444-8
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600

Contact details

Support:

For Support on this service: Please contact 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