Hello, One method would be to: determine if the SNP is in a coding region of a gene, find out the reading frame of the gene, examine the SNP location in the target codon, then compare the resulting amino acid translations. This would be the simple one-base substitution. For more complex substitutions, more than one amino acid may be added/deleted/changed and the analysis would be similar but likely involving more than one codon. Please see the dbSNP track's description page for the types of categories SNPs can sort into.
To view in the Browser, load your SNP dataset as a custom track and compare to the UCSC Genes track (or any Gene prediction track) zoomed in, with protein translation annotation on (set this on the track's description page). You could first filter the uploaded SNPs using an intersection function in the Table browser to create a track that only contains the SNPs in a coding region. Next, note the SNP location versus the gene's amino acids in the translation frame. Use an amino acid (aa) translation matrix to determine the aa when the alternate nucleotide is used and note if it is the same or different (synonymous or non-synonymous). Then at the next analysis level, determine if the new aa causes any significant changes in final protein product. More automated methods are possible but the basic analysis path is the same. Download/ftp gene track sequence (both mRNA and protein) from the browser and use your own tools to substitute the SNP base(s) in the mRNA. Then, do the translation in the Browser using DNA Duster (home page, left blue tool bar, click on Utilities, then DNA Duster) - be certain to use coding sequence only for accurate translations. Then run a protein vs protein comparison program (such as BLAT or other) between the proteins containing the SNP and those in the public domain and analyze differences. Some programs will also interpret synonymous aa as matches and non-synonymous aa as mis-matches depending on the program and any parameter files (protein matrix files, etc.) it uses. Or run a sequence comparison program with a mRNA (nucleotide) query containing your SNP(s) against an protein (aa) target (the "baseline or normal gene data set"). The program will do the translation of the query for you. Analyze differences Table browser: http://genome.ucsc.edu/cgi-bin/hgTables Data ftp instructions: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Please let us know if you have any questions about the UCSC Browser tools or data, Jennifer Jackson UCSC Genome Bioinformatics Group Clarence K. Zhang wrote: > Hello, > > > > We have a set of novel snp which have not been annotated in dbSNP or any > other public database. The only information we have is the base substitution > and its location. > > > > How can we determine whether or not it is a synonymous or non-synonymous > snp, from UCSC genome browser? > > > > > > Thank you very much, > > > > Clarence K. Zhang, PhD > Associate Research Scientist > Keck Biotechnology Laboratory Biostatistics Resource > Yale University School of Medicine > 300 George Street, Suite 503 > New Haven, CT 06511 > > 203-737-1123 (office) > [email protected] > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
