## Description

This track shows alignments between $organism radiation hybrid (RH) map sequences (consisting of ESTs and other genetic markers) and the genome. Many of these markers are not genetically polymorphic and therefore cannot be placed on genetic maps. The markers with RH map positions are useful for locating genes lying in genomic regions with mutations and in the positional cloning of zebrafish genetic mutants that exhibit interesting phenotypes.

8707 RH map sequences were aligned, consisting of:

- 2835 clone ends from Dr. Robert Geisler at the Max Planck Institute (MPI) for Developmental Biology, Germany and the Hubrecht Laboratory in the Netherlands
- 2015 ESTs from NCBI
- 171 RH shotgun sequences from Dr. Robert Geisler at the MPI and the Zebrafish Genome Initiative at Childrens Hospital, Boston
- 3686 WZ ESTs from WashU-Zebrafish Genome Resources

The majority of these sequences are single-read sequences in the range of about 40 - 1300 bp. The ESTs usually represent fragments of transcribed genes.

## Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated.

## Methods

To generate this track, $organism RH map sequences were aligned against the genome using blat. Only alignments with a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. The following pslReps parameters were used: -nearTop=0.0001 -minAli=0.96 -minCover=0.40.

## Credits

The $Organism RH Map track was produced by UCSC in collaboration with the Zebrafish Genome Initiative at Childrens Hospital, Boston, from sequence data obtained from the individuals and institutions mentioned in the Description section.