Hello, Thank you for your kind comments.
Tracks in the group Gene and Gene Predictions contain data that can be downloaded using the Table browser or using ftp to the Downloads server. The recommended track to start with for each species: For human and mouse, the track is "UCSC Genes" or "RefSeq Genes" (RefSeq is a subset of UCSC Genes, but has the potential to contain more data if it was released since UCSC Genes was last created). For rat, the track is "Known Genes" or "RefSeq Genes". Known Genes is similar to UCSC Genes (UCSC Genes is the newer, replacement, processing, not available for rat). For chicken, the track is "RefSeq Genes". No UCSC/Known Genes. To find out a description of these tracks (and all others), go into the Assembly and click on the track name. The creation date is noted here. Also from this page is a link "view table schema" that goes into the Table browser, starting at the primary table. This schema has the table associations and content descriptions. You can also just go into the Table browser and navigate to the track directly. Data can be output as sequence (reference genome, mRna, and protein) or as a single table or as a merge of associated tables & fields. File types are describes here (including genePred format): http://genome.ucsc.edu/FAQ/FAQformat.html For an example, if using Human and the UCSC Genes track, the primary table knownGene has transcript information (alignment to genome, with cds defined) in genePred format. Output can be just this table or selected fields from this table and associated tables or sequence (the types you mention). Some important associated tables for UCSC Genes are: kgAlias = Link together a Known Gene ID and a gene alias kgXref = Link together a Known Gene ID and a gene alias (more aliases) knownCanonical = Describes the canonical splice variant of a gene knownIsoforms = Links together various transcripts of a gene into a cluster Other help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html In particular, see these section to start with - Getting started on the Table Browser - Downloading genome data The actual data available for any genome or track can vary and the Table browser describes this. Some users use the Table browser for information, then ftp the tables goldenPath/<db>/database from the Downloads server (mySQL table == file name + .txt.gz for the data and +.sql for the schema) and manipulate the data locally. Sequence data is not kept in the mySQL tables - so use the Table browser or download from gbdb/<db>/<data files>. Hopefully this will get you started, Jen --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 3/4/10 6:52 AM, Dweep Harsh wrote: > Dear UCSC Team, > > Good Afternoon! First of all, I would like to congratulate UCSC team for > creating such a huge genomic database for scientific community for free. > I would like to ask you some queries related to all genes of human, > mouse, rat and chicken. > > 1. How can I download all mRNAs sequences of human, mouse, rat and > chicken with some information like Refseqid, length of mRNA sequence, > CDS (start and end position), Entrezid, Ensembl id, UCSC id (gene as > well as mRNA ids), Genesymbol (used in UCSC, NCBI and Ensembl databases) > etc. by using Genome browser or Table Browser ?? > > 2. Is it possible to download all the sequences (like upstreams, 5' > UTRs, CDSs and 3' UTRs) which are conserved among these species (human, > mouse, rat and chicken) by using UCSC database?? > > I am very much looking forward for your positive feedback. > > Thanks in advance! > > With Sincere Regards > Harsh Dweep > ZMF > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
