Hello Cynthia, Use the Table browser to extract this type of data. http://genome.ucsc.edu/cgi-bin/hgTables The top paragraph has help and tutorial links. Your basic steps will be to:
Find the gene: 1) set clade, genome, assembly and group=Gene and Gene Prediction 2) set track to UCSC Genes, RefSeq, or other that you know contains your target gene 3) set region if you know what it is, or paste the gene name/RefSeqID into the identifiers filter 4) output formats that are probably of most interest to you are the primary table, primary table + linked tables, fasta sequence (genomic, mRna, protein) or custom track Find sequences associated with the gene: 1) set clade, genome, assembly and group=mRna and Est (or any group of your choice) 2) set the track you are interested in gathering sequences from 3) again, set region if you know what it is, or use the intersection function against the custom track you created (above) 4) output formats are similar A gene prediction table contains coordinates for all exons, plus information about the coding region. Est/mRna tracks do not have coding regions specified. Comparing the genomic coordinates (using your own tools) between the two can allow the filtering of est/Mrna sequence coordinates to include only those covering the CDS. To find out the exact contents of any table, click on the "describe table schema" button next to the table name in the query page. If you do this for the primary/default table for a track, the bottom of the page will have the track's description info. File format help is available here: http://genome.ucsc.edu/FAQ/FAQformat. Genes will generally be in GenePred and the others PSL (BLAT alignment). And some coordinate help is here: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Try and please let us know if you need additional help with the specifics, Jennifer Jackson UCSC Genome Bioinformatics Group Cynthia Steiner wrote: > Dear all: > I would like to know if it is possible to export in a Fasta file a group > of sequences aligned for a specific gene. Also, is it possible to export > an alignment of sequences just including the coding region of the gene > of interest? > Thanks a lot for your help and reply. > Cynthia Steiner > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
