Repeat masking

Name	Last modified	Size
censor-norb-4.2.22.tar.gz	22-Mar-2010 13:45	807K
censor-norb-4.2.23.tar.gz	06-Apr-2010 10:50	767K
censor-norb-4.2.25.tar.gz	13-May-2010 11:57	775K
censor-norb-4.2.26.tar.gz	24-May-2010 20:56	769K
censor-norb-4.2.27.tar.gz	08-Jun-2010 21:31	1.5M
censor-norb-4.2.28.tar.gz	31-May-2012 23:04	1.4M
censor-4.2.22.tar.gz	22-Mar-2010 13:45	10.4M
censor-4.2.23.tar.gz	06-Apr-2010 10:50	9.0M
censor-4.2.25.tar.gz	13-May-2010 11:56	9.1M
censor-4.2.26.tar.gz	24-May-2010 20:56	9.1M
censor-4.2.27.tar.gz	08-Jun-2010 21:31	9.8M
censor-4.2.28.tar.gz	31-May-2012 00:12	15.6M

Description

censor compares and masks protein or nucleotide sequences.

There are 2 compilations of censor - one comes with a copy of repbase :

censor-v.v.vv.tar.gz

another one includes only software :

censor-norb-v.v.vv.tar.gz

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.

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

4.2.28
- Fixed a bug when in some cases a module that appends poly-A tail to ALU sequence would crash.

4.2.27
- Fixed bug with sequence masking

4.2.26
- Bug fixes
- Fixed several portability-related compilation issues
- Added coordinates to local alignment output

4.2.25
- Fixed a bug when censor crashed on short query sequences when attempting to extract fragments from it.
- Added option -copmact to produce compact version of map file.

4.2.23
- Replaced static linking with dynamic linking - that made censor compilable on MacOSX.
- Added experimental estimation of hit quality based on mismatches to transitions ratio. If the hit is of low quality (less than 100bp long and over 25% divergency) and ratio of mismathces to transition is above 2 - it is rejected as probable false positive.

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

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

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.