censor4.x - compares and masks protein or nucleotide sequences.

CENSOR without libraries of repeats

This version of censor does not include database of repetitive elements Repbase. The version of censor with a copy of Repbase can be downloaded below by registered users.

 Name                      Last modified      Size  Description
 censor-norb-4.2.22.tar.gz 16-Dec-2009 11:59  807K

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CENSOR with a copy of Repbase (registered users only)

 Name                      Last modified      Size  Description
 censor-4.2.22.tar.gz      16-Dec-2009 11:59  10.4M 

To install censor, you need to unpack archive file with distribution. Use

gunzip censor-xxx.tar.gz
tar xvf censor-xxx.tar

It will create directory censor-xxx. Follow instructions in file INSTALL in that directory.
* xxx - package version.

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

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.

Changelog

4.2.21 -> 4.2.22
- Forced proper handling of tab symbols in fasta definition line by blastall by adding "-J T" option.

4.2.20 -> 4.2.21
- Added handling of non-unix style ends of lines.

4.2.19 -> 4.2.20
- Modified parameters to blastall to give more consistent results with blastn algorithm. For some reason blastn program misses significant hits with wordsizes below 9. Wordsize (-W) is set to be 9-11 depending on sensitivity modes.