FASTM (Protein Databases)
FASTM --- compare peptides to a protein sequence database.
- Official Website
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
The databases to run the sequence similarity search against. Multiple databases can be used at the same time
|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|
|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|
|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.
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: PROTEIN [protein]
Step 3 - Parameters
The FASTA program to be used for the Sequence Similarity Search
|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]
The comparison matrix to be used to score alignments when searching the database
Default value is: MDM20 [M20]
- Additional information
Specify match/mismatch scores for DNA comparisons. The default is "+5/-4". "+3/-2" can perform better in some cases.
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
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) 
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: N/A [none]
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.|
|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
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]
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 email@example.com 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).