|
SNPs and Genomics
|
SNPs |
Import |
Import Affymetrix SNP array data and link to expression array data. |
Chromosomal display |
SNP locations are displayed on a chromosome ideogram, highlighting heterozygous loci. |
LOH |
Calculate loss-of-heterozygosity (LOH) probabilities across defined segments of the genome based on SNP data, and color-code on the chromosome ideogram.
Combine LOH data from multiple samples to indicate regions most commonly lost.
|
SNP info |
Summarize information on a single SNP: identifiers, location, flanking sequences, genotypes with race-specific allele frequencies and genotype allele frequencies in the data set and a test for Hardy-Weinberg equilibrium. |
Web link |
Link to TSC and dbSNP for further data on a SNP. |
Genomics |
Download |
Download genomic sequence for one, or a set of genes, from the Epicenter Software server. Sequence may include user-defined 5' and 3' extensions. Current genomes include human, mouse and rat. |
Display |
Selected genomic regions - one or more of the 5' sequence, the exons, the introns and the 3' sequence. Each sequence is shown schematically (indicating exonic regions) and by nucleotide. |
Align |
One or more sequence with a primary sequence, with or without gaps. Align Affymetrix probe sequences against the genomic sequence. Highlight mismatches. |
BLAST |
Click-and-drag to select a sequence and drop that sequence into a Web-based BLAST engine. |
Find |
Find all matches to a motif. The motif can include ambiguous nucleotides, variable length gaps, subregions of fixed sequence and others with a user-speified maximum mismatches. The motif can be a cobination of two or more alternatives. |
Motif list |
Build a library of nucleotide motifs of interest. |
Compare |
Count occurrences of a selected motif in a set of gene sequences, and statistically compare this to a control set. Search can be limited to conserved regions and/or non-repeat regions. |
Conserved |
|
Repeats |
|
|
|
