Thank you will it condense repeated or overlapping exons for different transcripts of a same gene? I would like to get the fasta from the 5'most exon to the 3'-most one
Vale -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Tuesday, November 23, 2010 5:41 PM To: Vasta, Valeria Cc: [email protected] Subject: Re: [Genome] (no subject) Hi Valeria, We do have one way to get this kind of output from the Table Browser, but it is limited to use with gene tables. That is, it can't be used directly with a custom track of coordinates. If you have a particular gene track in mind, select it in the Table Browser (you can still intersect the gene table with a custom track of coordinates, or paste a list of identifiers), then choose "CDS FASTA alignment from multiple alignment" as the output type. After hitting "get output" you will see several options for formatting the output, including whether to get amino acid or nucleotide sequence, whether to separate the the FASTA file by exons, and which species from the multiple alignment you would like included in the output. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/22/10 13:32, Vasta, Valeria wrote: > Hello > > > > Can you kindly let me know how to get from genes coordinates to a > multifasta file? > > thanks > > > > Valeria Vasta > > Assay Development Scientist | Biochemical and Molecular Genetics R&D > > Seattle Children's Research Institute > > 206-884-7674 OFFICE > > 206-987-7660 FAX > > [email protected] > > OFFICE 1900 9th Ave, Seattle, WA 98101 > > MAIL C9S-9 > > WWW seattlechildrens.org <http://seattlechildrens.org/> > > > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
