PSI-BLAST
Introduction
BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your novel sequence. Position specific iterative BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in which a profile is automatically constructed from the first set of BLAST alignments. PSI-BLAST is similar to NCBI BLAST2 except that it uses position-specific scoring matrices derived during the search, this tool is used to detect distant evolutionary relationships. PHI-BLAST functionality is available to use patterns to restrict search results.
- 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...)
- 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 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 |
| 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 |
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 openning 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 favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment.
Default value is: 1
- Additional information
Results E() 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: 10.0
PSSM E-Value cut-off
Expectation value threshold for automatic selection of matched sequences for inclusion in PSSM at each iteration.
Default value is: 1.0e-3
Scores
Maximum number of match score summaries reported in the result output.
Default value is: 500
Alignments
Maximum number of match alignments reported in the result output.
Default value is: 500
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 BLAST to only use residues 34 to 89, inclusive.
Default value is: START-END
Dropoff
The amount a score can drop before extension of word hits is halted
Default value is: 15 (default) [15]
Final Dropoff
Dropoff value for final gapped alignment
Default value is: 25 (default) [25]
Alignment Views
Formating for the alignments
| Name | Description | Value |
|---|---|---|
| pairwise | The query and match are output as a pairwsie alignment with a consensus line between the two sequences. In the consensus the match states are represented as: identical match as the base/residue, similarity as a '+' and missmatch as a space. | 0 |
| M/S identities | The matches found are shown relative to the ungapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line. | 1 |
| M/S non-identities | The matches found are shown relative to the ungapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line. | 2 |
| Flat identities | The matches found are shown relative to the gapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-). | 3 |
| Flat non-identities | The matches found are shown relative to the gapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-). | 4 |
Default value is: pairwise [0]
Checkpoint File Upload
Checkpoint file from the previous iteration. Must be in ASN.1 Binary Format.
Usage Mode For PHI-BLAST
Usage mode for PHI-BLAST functionality
| Usage Mode Name | Description | Value |
|---|---|---|
| blastpgp | This is the default PHIBLAST/BLASTPGP program mode, without patseedp or seedp options. | blastpgp |
| patseedp | This function takes three inputs, an input pattern, a query protein sequence with the pattern, and a protein sequence database. It identifies the pattern in the query and aligns the query against the database entries that contains the same pattern. It reports the pattern position in the query, the total number of pattern occurrences in the database, and the actual database entries with pattern and alignment to the input query. Specifically, it reports the seqid of the database entry, its alignment (with the query) E-value, scores, and pattern position. | patseedp |
| seedp | Restrict the search for local alignments to a subset of the pattern occurrences in the query. This program option requires the user to specify the location(s) of the interesting pattern occurrence(s) in the pattern file (for the syntax see below). When there are multiple pattern occurrences in the query it may be important to decide how many are of interest because the E-value for matches is effectively multiplied by the number of interesting pattern occurrences. | seedp |
Default value is: blastpgp
Pattern File Upload
Pattern file for PHI-BLAST functionality. This file needs to be in the style of a prosite entry file, with at least an ID line, PA line and optional HI line.
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 test@altoromutual.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).