Repbase

Repeat masking

Name	Last modified	Size
censor-4.2.31.tar.gz	17-Jan-2025 03:17	1.3M

Description

censor compares and masks protein or nucleotide sequences.

You need to install wu-blast or legacy ncbi-blast package to use censor.

Repbase

If you have a subscription to repbase, you can download FASTA-formatted repbase and copy it to censor installation directory, e.g. /usr/local/censor-4.2.31/share/censor-4.2.31/biolib/

Censor package includes two scripts. One, called censor, is designed to run with the licensed, full-featured version of wu-blast (censor was tested with wu-blast that was available from Washington University before it was sold to Advanced Biocomputing, LLC). Another executable, censor.ncbi, has settings modified to work with ncbi-blast.

Looks like wu-blast, now ab-blast, is no longer available for free for academic users. For those users who don't have wu-blast the only way to use censor is to use censor.ncbi. Your feedback is welcomed to improve censor's performance with ncbi-blast.

References

Kohany O, Gentles AJ, Hankus L, Jurka J
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474

Changelog

4.2.31
- Few bug fixes