SECRETOOL HELP
You will
find HELP for the different functional menu sections of the web-tool.
- 0. Mandatory requirements.
- 1. PIPELINE TOOL.
- 2. LOCAL TOOLS.
- 2.1. SecretomeP v.1.0
- 2.2. TargetP v.1.1
- 2.3. SignalP v.4.0
- 2.4. TMHMM v.2.0
- 2.5. Local Sequence Retriever.
- 2.6. WoLFPSORT v.2.0
- 2.7. Local BLAST.
- 2.8. Local HMM search.
- 2.9. PredGPI parser.
- 3. REMOTE TOOLS.
Sequence
files to be used as input must be in FASTA format.
The following extensions (.fasta; .fa; .faa ; .fas; .fna;
.sequences; .txt) will be recognized by our tool. In case your FASTA file has
any other extension, just rename it to any of the mentioned extensions.
Please, avoid blank spaces in your input file name (e.g. input file name.fasta -> input_file_name.fasta) and the
following illegal characters: ~ # % & * { } \ : < > ¿ / + | " . ( ) = ? / , ; ' `
In order to perform a complete secretome analysis in an intuitive and user friendly
manner, we developed a single step query interface.
-Upload a query file in FASTA format
-Enter a valid
e-mail address
-Select the cut-off scores for the processing tools
(or run them on default values)
-Submit your
data
-Download your
results from the url received by email or displayed on the screen.
*The result of the whole pipeline are
just 3 plain text files, containing
the putative secreted protein sequences in FASTA format, the BLAST output displaying putative functions and ortholog relations with other fungi and the HMMer3 output to infer the Pfam
domains.
There are a number of tools that work independently for secreted proteins
prediction.
*SecretomeP
v.1.0
For ab initio predictions of non-classical secreted proteins we
chose to add SecretomeP as individual tool. It also
allows the use of a full proteome as input, enables
the user to define a confidence probability and retrieves a list
containing all the putative secreted proteins detected results over that
probability. .
How to use:
-Enter your FASTA
-Select cut-off probability
-Submit!
-Download your
results from the url received by email or displayed on the screen.
TargetP tool was specifically developed to
enhance TargetP analysis, by allowing the input of a
full proteome FASTA in a single step. It enables the user to define a cut-off
probability and then retrieves all the secreted detected results over that
probability.
How to use:
-Enter your FASTA
-Select cut-off probability
-Submit!
-Download your
results from the url received by email or displayed on the screen.
As the
previous tool, this one was developed to enhance SignalP
prediction process. It also allows the use of a full proteme
as input and enables the user to define a confidence probability and
then retrieves all the putative secreted proteins detected results over that
probability.
How to use:
-Enter your FASTA
-Select cut-off probability
-Submit!
-Download your
results from the url received by email or displayed on the screen.
Once again
we present a tool with no limited number of sequences as input. It also permits
to define the number of transmembrane domains to use
as cut-off , and then retrieves all the candidates
with a number of transmembrane domais
equal or lower to that score.
How to use:
-Enter your FASTA
-Select maximun number of Transmembrane
Domains
-Submit!
-Download your
results from the url received by email or displayed on the screen.
As its name
suggests, through this program we can retrieve a list of sequence IDs from a
big FASTA containing them among thousands of other sequences.
How to use:
-Enter list of IDs to
retrieve
- Enter FASTA file containing
list IDs in the FASTA headers in the same notation
-Submit!
-Download your
results from the url received by email or displayed on the screen.
This tool
predicts proteins subcellular location, specifically
if a protein is putatively secreted. It enables the user to define a cut-off
scrore and then retrieves all the proteins detected
as candidates for secretion over the cut-off value.
How to use:
-Enter your FASTA
-Select cut-off score
-Submit!
-Download your
results from the url received by email or displayed on the screen.
The NCBI nr proteins database is available
to perform BLASTp/BLASTx searches under user defined
e-value.
How to use:
-Enter your FASTA
-Select BLAST program (BLASTp or BLASTx)
-Select cut-off value
-Submit!
-Download your
results from the url received by email or displayed on the screen.
Both PfamA and PfamB hmm profiles
databases have been enabled for searches on user sets of study.
How to use:
-Enter your FASTA
-Select domains database to search against
-Select cut-off value
-Submit!
-Download your
results from the url received by email or displayed on the screen.
This parser
was developed to enhance PredGPI result reports
parsing. It enables the user to define a confidence probability and then
retrieves all the putatively GPI membrane anchored proteins detected with a
score under that probability. This tool is specially efficient and time saving
when managing reports with a high number of results.
How to use:
-Enter your predictions file
(files parsed are only those in the format obtained by clicking "Download" in PredGPI)
-Select cut-off probability
-Submit!
-Download your
results from the url received by email or displayed on the screen.
A
collection of links to sequence analysis tools for secretomes
are available in this section to grant a rapid access to them.
Included
tools are:
-Target P: Predicts the subcellular location of eukaryotic proteins by the presence N-terminal presequences
-SignalP: Predicts
the subcellular location of eukaryotic proteins by prediction of signal peptide cleavage sites
-Secretome P:
Produces ab initio predictions of non-classical i.e. not
signal peptide triggered protein secretion.
-TMHMM: Predicts the presence of transmembrane domains in protein sequences.
-WoLFPSORT: Predicts
the subcellular location of proteins. In this case we
are interested on putatively secreted proteins
-Remote BLAST:
The well known pairwise local alignment search tool.
-Remote HMMer:
The well known pairwise local alignment search tool.
-PredGPI: Predicts
GPI membrane anchored proteins. It allows the use up to 500 sequences at a
time.
-MUSCLE & CLUSTALW: Two of the most
popular multiple sequence alignment tools.
-CDD: The conserved domain database tool to
predict functional domains on protein sequences.
-Phylemon2:
A suite of
web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
How
to use the REMOTE tools
-Just click
on the tool on the menu, then the tool webpage will open in a new window and
then you are ready to enjoy the experience.
