CENSOR

Introduction

CENSOR is a software tool which screens query sequences against a reference collection of repeats and "censors" (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.

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 - Taxon database

Databases

Database

Database Name Description Abbreviation
Conserved repeats conserved
...Eukaryota Eukaryota
......Fungi Fungi
......Schmidtea mediterranea Schmidtea_mediterranea
......Vertebrata Vertebrata
.........Takifugu Takifugu
.........Danio rerio (Zebrafish) Danio_rerio
.........Mammalia Mammalia
............Carnivora Carnivora
...............Canis lupus familiaris Canis_lupus_familiaris
...............Felis catus (Cat) Felis_catus
............Cetartiodactyla Cetartiodactyla
...............Bos taurus (Cow) Bos_taurus
...............Sus scrofa (Pig) Sus_scrofa
............Primates Primates
...............Homo sapiens (Human) Homo_sapiens
............Rodentia (Rodents) Rodentia
...............Mus musculus (Mouse) Mus_musculus
...............Rattus (Rat) Rattus
............Monodelphis domestica Monodelphis_domestica
.........Gallus gallus (Chicken) Gallus_gallus
.........Xenopus Xenopus
......Ascidiacea (Sea squirts) Ascidiacea
.........Ciona intestinalis Ciona_intestinalis
.........Ciona savignyi Ciona_savignyi
......Arthropoda Arthropoda
.........Hexapoda (Insects) Hexapoda
............Drosophila (Fruit flies) Drosophila
............Anopheles (Mosquitos) Anopheles
......Caenorhabditis elegans (Nematode) Caenorhabditis_elegans
......Nematostella vectensis Nematostella_vectensis
......Viridiplantae (Green plants) Viridiplantae
.........Poaceae (Grass family) Poaceae
............Oryza (Rice) Oryza
............Panicoideae (Maize, sugar cane, sorghum, millet) Panicoideae
............Triticum (Wheats, barleys, ryes) Triticum
.........Arabidopsis thaliana (Thale cress) Arabidopsis_thaliana
......Thalassiosira pseudonana (Diatom) Thalassiosira_pseudonana

Default value is: ...............Homo sapiens (Human) [Homo_sapiens]

Step 2 - Input Sequences

Input Sequence

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. There is a limit of 1MB for the sequence entry.

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 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. There is a limit of 1MB for the sequence entry.

Step 3 - Parameters

Mode

Mode.

Mode Name Value
Rough rough
Normal norm
Sensitive sens

Default value is: Normal [norm]

Translate

Translate.

Default value is: no [false]

identity

Identity.

Default value is: no [false]

Show simple

Show simple.

Default value is: no [false]

Mask pseudogenes

Mask pseudogenes.

Default value is: no [false]

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).

References

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
(2006) BMC bioinformatics 7 :474
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 Apr 06) Nucleic acids research
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