PSI-Search
Introduction
PSI-Search, similar to PSI-BLAST, combines the Smith-Waterman search algorithm with the PSI-BLAST profile construction strategy to find distantly related protein sequences. Searches are done with SSEARCH, and the selected hits are combined with BLASTPGP to build a position specific scoring matrix (PSSM), which is then used for another search with SSEARCH in the next iteration.
- FAQs
- 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
Databases
The databases to run the sequence similarity search against. Multiple databases can be selected 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 Reference Proteomes | Taxonomic subset of the UniProtKB Reference Proteomes | uniprotkb_reference_proteomes |
| RefProtDom 3 | Reference Protein Domains 3 - A protein database with improved domain boundaries and homology relationships. | rpd3 |
| 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 Intelectual 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 |
| Others 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 |
Step 2 - Sequence
Sequence Input Window
The query sequence can be entered directly into this form. The sequence can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot 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, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) 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.
Step 3 - Parameters
Matrix
The comparison matrix to be used to score alignments when searching the database
| Matrix Name | Abbreviation |
|---|---|
| BLOSUM45 | BLOSUM45 |
| BLOSUM62 | BLOSUM62 |
| BLOSUM80 | BLOSUM80 |
| PAM30 | PAM30 |
| PAM70 | PAM70 |
Default value is: BLOSUM62
- Additional information
Gap Open Penalty
Penalty taken away from the score when a gap is created in sequence. Increasing the gap opening penalty will decrease the number of gaps in the final alignment.
Default value is: 11
- Additional information
Gap Extend Penalty
Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favours short gaps in the final alignment, conversly, decreasing the gap extension penalty favours long gaps in the final alignment.
Default value is: 1
- Additional information
HOE Region Masking
Turn on/off the sequence masking for HOEs in PSSM constructions. This option allows you to mask sequence characters beyond the alignment region when constructing the PSSM, reducing over-extension errors.
Default value is: yes [true]
Results E() Limit
Limits the number of scores and alignments reported based on the expectation value. This value is the maximum number of times the match is expected to occur by chance.
Default value is: 10.0
PSSM E-Value cut-off
Expectation value threshold for automatic selection of matched sequences for inclusion in the PSSM at each iteration.
Default value is: 1.0e-3
Scores
Maximum number of alignment score summaries reported in the result output.
Default value is: 500
Alignments
Maximum number of alignments reported in the result output.
Default value is: 500
Multi HSPs
Turn on/off the display of all significant alignments between query and database sequence.
Default value is: no [false]
Score Format
Different score formats.
Default value is: Default [default]
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.
| Program Name | Description | Abbreviation |
|---|---|---|
| none | No filtering of the query sequence. | none |
| seg | Uses the SEQ filter (Wootton and Federhen, 1993) to replace low-complexity regions with 'X' in protein query sequences. | seg |
| xnu | Uses the XNU filter (Claverie and States, 1993) to mask statistically significant tandem repeats in protein query sequences. | xnu |
| seg+xnu | Uses both SEG and XNU to filter low-complexity regions and statistically significant tandem repeats in protein query sequences. | seg+xnu |
Default value is: none
Histogram
Turn on/off the histogram in the PSI-Search 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]
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.
Default value is: no [false]
Checkpoint File Upload
Checkpoint file from the previous iteration. Must be in ASN.1 Binary Format.
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 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
Contact details
- Support:
-
For Support on this service: Please contact EMBL-EBI support at https://www.ebi.ac.uk/support/FASTA
- The Author:
-
William R. Pearson
Department of Biochemistry
Box 440, Jordan Hall
U. of Virginia
Charlottesville, VA