How To Find The Oriantation Of The Repeats Downloaded From Ucsc

Question

[roll]

Hi,

I downloaded the repeats from UCSC repeatMasker as fa.out files and converted them to bed files simply using awk. I am now trying to determine the the orientation of the repeats. I know that i can check this with regard to the start and end position. Looking at this data seems that all my start position is lower than the end position suggesting that all my repeats are on positive strand? I might be wrong but this does not sound right. Can that be true that all repeats are on positive strand? Or am i missing something important here?

[Devon Ryan]

The reverse complement of a repeat is still a repeat.

[Michael]

Repeat sequences are not strand specific, but always given on forward strand, I think that was what you are missing ;)

Answer 1

[Pierre Lindenbaum]

For the simple Repeats , That information doesn't seem to be available. And as said Michael, in the UCSC, any feature have chromStart<=chromEnd.

$ curl -s http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/simpleRepeat.sql
-- MySQL dump 10.10
--
-- Host: localhost    Database: mm9
-- ------------------------------------------------------
-- Server version    5.0.21

/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;

--
-- Table structure for table `simpleRepeat`
--

DROP TABLE IF EXISTS `simpleRepeat`;
CREATE TABLE `simpleRepeat` (
  `bin` smallint(5) unsigned NOT NULL default '0',
  `chrom` varchar(255) NOT NULL default '',
  `chromStart` int(10) unsigned NOT NULL default '0',
  `chromEnd` int(10) unsigned NOT NULL default '0',
  `name` varchar(255) NOT NULL default '',
  `period` int(10) unsigned NOT NULL default '0',
  `copyNum` float NOT NULL default '0',
  `consensusSize` int(10) unsigned NOT NULL default '0',
  `perMatch` int(10) unsigned NOT NULL default '0',
  `perIndel` int(10) unsigned NOT NULL default '0',
  `score` int(10) unsigned NOT NULL default '0',
  `A` int(10) unsigned NOT NULL default '0',
  `C` int(10) unsigned NOT NULL default '0',
  `G` int(10) unsigned NOT NULL default '0',
  `T` int(10) unsigned NOT NULL default '0',
  `entropy` float NOT NULL default '0',
  `sequence` longblob NOT NULL,
  KEY `chrom` (`chrom`(16),`bin`),
  KEY `chrom_2` (`chrom`(16),`chromStart`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;

/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;

-- Dump completed on 2007-08-22 17:55:42