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.
- 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).