Hi L. G., We get mRNA sequences from GenBank and align them to the reference genome. There are two different ways to get sequence, depending on whether you want the mRNA sequence or the genomic sequence that corresponds to the places that the mRNAs aligned.
To get the mRNA sequences, you will need to download the file of all mRNA sequences from GenBank and parse out the ones you want. You can get the file by clicking on the homepage, and then Downloads -> (organism of interest) -> Full data set -> mrna.fa.gz. If you want genomic sequence for a list of identifiers, you can download it for selected mRNAs via the Table Browser in FASTA format. To do this, hit the blue "Tables" link at the top of the page (which will take you to http://genome.ucsc.edu/cgi-bin/hgTables), select the clade/genome/assembly you wish to use, and then choose: group: mRNA and EST tracks track: choose "(organism) mRNAs" table: all_mrna or mrna region: genome identifiers: paste/upload a list of identifiers here output format: sequence output file: enter a file name if you want to save the results locally When you hit "get output" you will see a number of options for formatting your FASTA file. I hope this is helpful. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group Bentley, Gordon wrote on 10/4/10 3:24 PM: > We need to download the mRNA sequences for all the genes in a > specific gene family, preferably as one list of FASTA formatted sequences. > > Can you tell us how to do this? > > Much thanks, > > L. G. Bentley > ARI/UCSF > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
