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Repeat masking
Name |
Last modified |
Size |
censor-norb-4.2.22.tar.gz |
02-Feb-2017 21:59 |
807K |
censor-norb-4.2.23.tar.gz |
02-Feb-2017 21:59 |
767K |
censor-norb-4.2.25.tar.gz |
02-Feb-2017 21:59 |
775K |
censor-norb-4.2.26.tar.gz |
02-Feb-2017 21:59 |
769K |
censor-norb-4.2.27.tar.gz |
02-Feb-2017 21:59 |
1.5M |
censor-norb-4.2.28.tar.gz |
02-Feb-2017 21:59 |
1.4M |
censor-norb-4.2.29.tar.gz |
02-Feb-2017 21:59 |
1.4M |
censor-norb-4.2.30.tar.gz |
04-Dec-2023 22:27 |
1.4M |
censor-4.2.22.tar.gz |
02-Feb-2017 21:59 |
10.4M |
censor-4.2.23.tar.gz |
02-Feb-2017 21:59 |
9.0M |
censor-4.2.25.tar.gz |
02-Feb-2017 21:59 |
9.1M |
censor-4.2.26.tar.gz |
02-Feb-2017 21:59 |
9.1M |
censor-4.2.27.tar.gz |
02-Feb-2017 21:59 |
9.8M |
censor-4.2.28.tar.gz |
02-Feb-2017 21:59 |
15.6M |
censor-4.2.29.tar.gz |
02-Feb-2017 21:59 |
23.1M |
censor-4.2.30.tar.gz |
04-Dec-2023 22:22 |
62.5M |
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.gzanother 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 JAnnotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474
Changelog
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.
