USCS Map viewer
Finding a region by map position
This is the infamous site written by Jim Kent, a graduate student. Read about it at the NY Times
You can access this site at UCSC
To browse the genome, access this site
We are going to access the region on chromosome 4 from 61M to 63M. Copy this and paste it into the box:
chr4:61000000-63000000
You will see something like this:
The image contains:
- Base position: position along the chromosome in bp
- Chromosome Band: Approximate cytogenetic maps
- STS Markers: STS markers on genetic and RH maps
- Gap: locations of unsequenced regions
- Coverage: Locations of sequenced regions
- Acembly Genes: Genes reconstructed solely from mRNA and EST data
- Ensembl Genes: Genes from ENSEMBL
- Fgenesh++ Genes: Genes from Softberry based on hidden Markov models (HMM) and protein similarity
- Spliced ESTS: A "highly relevant" subset of human ESTs, those that are spliced
- UniGene: UniGene clusters of ESTs aligned to the genome
- Nonhuman mRNA: GenBank mRNAs from other species aligned with the genome
- Mouse BLAT: Alignments of mouse genome to human. i.e. synteny
- Fish BLAT: Conserved regions, generally protein-coding homologs, from a genomics project of long random reads in the pufferfish, Tetraodon nigroviridis.
- FISH clones: fluorescence in situ hybridization placed clones
- Overlap SNPs: Single nucleotide polymorphisms found on overlapping contigs
- Random SNPs: Single nucleotide polymorphisms found by random sequencing that are useful markers in mapping genes and complex traits
- RepeatMasker: Dispersed repeats determined byRepeatMasker.
Homology Searches
This is the sqeuence that we used in the last search.
Jim Kent wrote the BLAT search engine. Not to be confused with BLAST, BLAT is a more efficient system for comparing sequences.
You can access the BLAT engine directly. Paste the sequence in, and click the submit button. You will get a list of hits. Note they are sorted by score, and the best hit is at the top.
Synteny Maps
There is no direct way to look for synteny, rather all the maps display synteny by default