FingerPRINTScan

Introduction

Search against FingerPRINTScan with a protein query sequence to identify the closest matching PRINTS sequence motif fingerprints in a protein sequence. Identifies a queried protein sequence as a member of a known family, infering a wealth of known information pertinent to that family and its members. FingerPRINTScan classifies sequences using familial definitions from the PRINTS database, allowing progress to be made with the identification of distant evolutionary relationships. The approach makes use of the contextual information inherent in a multiple-motif method, and has the power to identify hitherto unidentified relationships in mass genome data.

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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 - Input Sequences

Input Sequence

The input sequence can be entered directly into this form. The sequence can be be in FASTA 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 valid sequence in FASTA or UniProtKB/Swiss-Prot format can be used as input. Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters.

Step 2 - Set Matrix options

Distance Deviation

Percentage distance deviation allowed between motifs. The number is in the range 0 .. 100. (0 is a special case which turns off distance checking)

Default value is: 10

Result Views

Output result views.

View Name Value Description
Brief 8 Shortest description of the results, only the top scoring hits.
Concise 4 Medium description of the results, the ten top scoring hits detailed by fingerprint.
Detailed 2 Most detailed description of the results, the ten top scoring hits, detailed by individual motif.
w/Alignments 1 EXPERIMENTAL alignment of the sequence and the consensus sequence of the motif.(-a flag needs to be on too).

Default value is: w/Alignments [1]

Expectation Value

The Expectation value cut-off for hits during the scan. This number is a real number.

Default value is: 0.0001

Data Matrix

The data matrix to search.

Matrix Name Value
PRINTS BLOSUM62 prints.pval_blos62
PRINTS BLOSUM45 prints.pval_blos45
PRINTS BLOSUM80 prints.pval_blos80

Default value is: PRINTS BLOSUM62 [prints.pval_blos62]

Step 3 - 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

PRINTS-S: the database formerly known as PRINTS.
(2000 Jan 01) Nucleic acids research 28 (1) :225-7
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600