Description
This track shows alignments between zebrafish T51 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.
This track shows alignments for 11514 RH map sequences (October 3, 2006
update) that consist of:
The linkage group number is equivalent to the chromosome number for zebrafish.
Position, which is relative to the top of the linkage group, is the marker
number used by the SAMapper software. Marker types can be BAC_END, EST, GENE,
SSLP or STS. The markers are from the following sources:
- BACENDS - end sequences of fingerprinted BAC clones.
- CUSTOM - various markers and genes sent from outside labs to CHBG for
mapping.
- INSERTMUT - genomic sites where retroviral insertions occurred in
insertional mutants.
- MGH - SSLP markers from the lab of Dr. Mark Fishman at Massachusetts
General Hospital.
- NCBI - marker primer or parent sequences retrieved from the NCBI
databases.
- OTHER_ZFEST - zebrafish ESTs generated elsewhere other than the
Washington
University Genome Center at St. Louis.
- SEQPROJ - contig or scaffold from the zebrafish genome sequencing
project at The Wellcome Trust Sanger Institute.
- SHOTGUN - random shotgun sequences from
The Wellcome Trust Sanger Institute.
- THISSE - cDNAs that have specific expression patterns found by
in situ hybridization and provided from the lab of Drs. Bernard and
Christine Thisse at the Institute of Genetics and Molecular and Cellular Biology.
- WU_ZFEST - individual ESTs and EST assemblies from the
Washington University Genome Center at St. Louis.
- WZ - EST assemblies from the Washington University Genome Center at
St. Louis.
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, zebrafish 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 80% base identity with the genomic sequence were kept.
The following pslReps parameters were used: -nearTop=0.0001 -minAli=0.80
-minCover=0.20.
Credits
The zebrafish RH Map track was produced by UCSC in collaboration with the
Zebrafish Genome Project Initiative at Childrens Hospital, Boston, from
sequence data obtained from the individuals and institutions mentioned in the
Description section.
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