FASTM (Protein 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
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
UniProtKB Taxonomic Subsets
UniProtKB Archaea Taxonomic subset of the UniProt Knowledgebase for archaea uniprotkb_archaea
UniProtKB Arthropoda Taxonomic subset of the UniProt Knowledgebase for arthropoda uniprotkb_arthropoda
UniProtKB Bacteria Taxonomic subset of the UniProt Knowledgebase for bacteria uniprotkb_bacteria
UniProtKB Complete Microbial Proteomes Taxonomic subset of the UniProt Knowledgebase for complete microbial proteomes uniprotkb_complete_microbial_proteomes
UniProtKB Eukaryota Taxonomic subset of the UniProt Knowledgebase for eukaryota uniprotkb_eukaryota
UniProtKB Fungi Taxonomic subset of the UniProt Knowledgebase for fungi uniprotkb_fungi
UniProtKB Human Taxonomic subset of the UniProt Knowledgebase for human uniprotkb_human
UniProtKB Mammals Taxonomic subset of the UniProt Knowledgebase for mammals uniprotkb_mammals
UniProtKB Nematoda Taxonomic subset of the UniProt Knowledgebase for nematoda uniprotkb_nematoda
UniProtKB PDB Taxonomic subset of the UniProt Knowledgebase for PDB uniprotkb_pdb
UniProtKB Rodents Taxonomic subset of the UniProt Knowledgebase for rodents uniprotkb_rodents
UniProtKB Vertebrates Taxonomic subset of the UniProt Knowledgebase for vertebrates uniprotkb_vertebrates
UniProtKB Viridiplantae Taxonomic subset of the UniProt Knowledgebase for viridiplantae uniprotkb_viridiplantae
UniProtKB Viruses Taxonomic subset of the UniProt Knowledgebase for viruses uniprotkb_viruses
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 100% (SEG filtered) UniProt Reference Clusters database (SEG filtered) with entries that have 100% mutual sequence identity. uniref100_seg
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
Patents
EPO Patent Protein Sequences Protein sequences appearing in patents from the European Patent Office (EPO) epop
JPO Patent Protein Sequences Protein sequences appearing in patents from the Japanese Patent Office (JPO) jpop
KIPO Patent Protein Sequences Protein sequences appearing in patents from the Korean Intellectual Property Office (KIP0). kpop
USPTO Patent Protein Sequences Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO) uspop
NR Patent Proteins Level-1 Non-redundant Patent Protein sequences Level 1 covering data from the EPO, JPO, KIPO and USPTO nrpl1
NR Patent Proteins Level-2 Non-redundant Patent Protein sequences Level 2 covering data from the EPO, JPO, KIPO and USPTO nrpl2
Structure
Protein Structure Sequences Protein sequences from structures described in the Brookhaven Protein Data Bank (PDB) pdb
Structural Genomics Targets Structural Genomic Targets (SGT) database sgt
Other Protein Databases
UniProt Archive The UniProt Archive (UniParc) contains available protein sequences collected from many different sources. The sequence data are archived to facilitate examination of changes to sequence data. Search UniParc if you want to examine the "history" of a particular sequence. uniparc
IntAct The IntAct sequence database is derived from UniProt entries and data from MassSpec experiments submitted to the IntAct protein-interaction database. intact
IMGT/HLA The human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) database. imgthlap
IPD-KIR Human Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD) ipdkirp
IPD-MHC Major Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD) ipdmhcp

Default value is: UniProt Knowledgebase [uniprotkb]

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
PROTEIN protein

Default value is: PROTEIN [protein]

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
FASTF Compare mixed ordered peptides (Edman degredation) to a protein sequence database. fastf
FASTS Compare unordered peptides (mass-spec. analysis) to a protein sequence database. fasts

Default value is: FASTM [fastm]

Matrix

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

Matrix Name Abbreviation
BLOSUM50 BL50
BLOSUM62 BL62
BLASTP62 BP62
BLOSUM80 BL80
PAM120 P120
PAM250 P250
MDM10 M10
MDM20 M20
MDM40 M40

Default value is: MDM20 [M20]

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
N/A none

Gap Open Penalty

Score for the first residue in a gap.

Default value is: -10

Additional information

Gap Extend Penalty

Score for each additional residue in a gap.

Default value is: -2

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: N/A [none]

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.
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.

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 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]

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 February) 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 April) Proceedings of the National Academy of Sciences of the United States of America 85 (8) :2444-8
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) 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