PSISearch2
Introduction
PSISearch2D automates successive iterations of "psiblast" or "ssearch36" using different strategies to reduce PSSM contamination from alignment over-extension. "psisearch2_msa.pl" uses the "m89_btop_msa2.pl" program to read BTOP formatted output from "psiblast" or "ssearch36" and produce both a multiple sequence alignment (MSA) and a fasta formatted custom database of the sequences in the MSA. "psiblast" then produces a PSSM From the MSA and custom database.
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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 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 |
| 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 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 |
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
Iteration Program
Select the program used for searching.
| Program Name | Description | Abbreviation |
|---|---|---|
| SSEARCH | Compare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm. | ssearch |
| PSIBLAST | NCBI PSIBLAST program | psiblast |
| GGSEARCH | Compare a protein or DNA sequence to a sequence database using a global-global alignment (Needleman-Wunsch) | ggsearch |
| GLSEARCH | Compare a protein or DNA sequence to a sequence database using a global-local alignment | glsearch |
Default value is: SSEARCH [ssearch]
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
Max Iteration Number
Run iteration(s) until reaching convergence or the maximum number of iterations.
Default value is: 3 (default) [3]
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).